Browsing by Author "Rinn, John"

Now showing items 1-20 of 35

    • Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits 

      Choudhuri, Avik; Trompouki, Eirini; Abraham, Brian J.; Colli, Leandro M.; Kock, Kian Hong; Mallard, William; Yang, Min-Lee; Vinjamur, Divya S.; Ghamari, Alireza; Sporrij, Audrey; Hoi, Karen; Hummel, Barbara; Boatman, Sonja; Chan, Victoria; Tseng, Sierra; Nandakumar, Satish K.; Yang, Song; Lichtig, Asher; Superdock, Michael; Grimes, Seraj N.; Bowman, Teresa V.; Zhou, Yi; Takahashi, Shinichiro; Joehanes, Roby; Cantor, Alan; Bauer, Daniel; Ganesh, Santhi K.; Rinn, John; Albert, Paul S.; Bulyk, Martha; Chanock, Stephen J.; Young, Richard; Zon, Leonard (Springer Science and Business Media LLC, 2020-11-23)
      Genome-wide association studies (GWAS) reveal genomic variants associated with human traits and diseases. Most trait-associated variants are located within cell type-specific enhancers, but the molecular mechanism by which ...

    • CRISPR Display: A modular method for locus-specific targeting of long noncoding RNAs and synthetic RNA devices in vivo 

      Shechner, David M.; Hacisüleyman, Ezgi; Younger, Scott T.; Rinn, John L. (2016)
      Noncoding RNAs (ncRNAs) comprise an important class of regulatory molecules that mediate a vast array of biological processes. This broad functional capacity has also facilitated the design of artificial ncRNAs with novel ...

    • Differential Gene and Transcript Expression Analysis of RNA-seq Experiments with TopHat and Cufflinks 

      Trapnell, Cole; Roberts, Adam; Goff, Loyal; Pertea, Geo; Kim, Daehwan; Kelley, David Roy; Pimentel, Harold; Salzberg, Steven L.; Rinn, John L; Pachter, Lior (Nature Publishing Group, 2012)
      Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments ...

    • The Discovery and Characterization of the lncRNA Firre 

      Hacisuleyman, Fatma Ezgi (2015-05-08)
      RNAs, including long noncoding RNAs (lncRNA), are known to be abundant and important structural components of the nuclear infrastructure. Yet, the identities, functional roles, and localization dynamics of lncRNAs that ...

    • Diverse Phenotypes and Specific Transcription Patterns in Twenty Mouse Lines with Ablated LincRNAs 

      Lai, Ka-Man Venus; Gong, Guochun; Atanasio, Amanda; Rojas, José; Quispe, Joseph; Posca, Julita; White, Derek; Huang, Mei; Fedorova, Daria; Grant, Craig; Miloscio, Lawrence; Droguett, Gustavo; Poueymirou, William T.; Auerbach, Wojtek; Yancopoulos, George D.; Frendewey, David; Rinn, John; Valenzuela, David M. (Public Library of Science, 2015)
      In a survey of 20 knockout mouse lines designed to examine the biological functions of large intergenic non-coding RNAs (lincRNAs), we have found a variety of phenotypes, ranging from perinatal lethality to defects associated ...

    • DNMT1-interacting RNAs block gene specific DNA methylation 

      Di Ruscio, Annalisa; Ebralidze, Alexander K.; Benoukraf, Touati; Amabile, Giovanni; Goff, Loyal A.; Terragni, Joylon; Figueroa, Maria Eugenia; De Figureido Pontes, Lorena Lobo; Alberich-Jorda, Meritxell; Zhang, Pu; Wu, Mengchu; D’Alò, Francesco; Melnick, Ari; Leone, Giuseppe; Ebralidze, Konstantin K.; Pradhan, Sriharsa; Rinn, John L.; Tenen, Daniel G. (2013)
      Summary DNA methylation was described almost a century ago. However, the rules governing its establishment and maintenance remain elusive. Here, we present data demonstrating that active transcription regulates levels of ...

    • Function and evolution of local repeats in the Firre locus 

      Hacisuleyman, Ezgi; Shukla, Chinmay J.; Weiner, Catherine L.; Rinn, John L. (Nature Publishing Group, 2016)
      More than half the human and mouse genomes are comprised of repetitive sequences, such as transposable elements (TEs), which have been implicated in many biological processes. In contrast, much less is known about other ...

    • A Global Transcriptional Analysis of Plasmodium Falciparum Malaria Reveals A Novel Family of Telomere-Associated lncRNAs 

      Broadbent, Kate Mariel; Park, Daniel John; Wolf, Ashley Robin; Van Tyne, Daria Natalie; Sims, Jennifer Sung; Ribacke, Ulf Erik; Cooke, Sarah Volkman; Duraisingh, Manoj T.; Wirth, Dyann Fergus; Sabeti, Pardis Christine; Rinn, John L (BioMed Central, 2011)
      Background: Mounting evidence suggests a major role for epigenetic feedback in Plasmodium falciparum transcriptional regulation. Long non-coding RNAs (lncRNAs) have recently emerged as a new paradigm in epigenetic ...

    • The histone chaperone CAF-1 safeguards somatic cell identity 

      Cheloufi, Sihem; Elling, Ulrich; Hopfgartner, Barbara; Jung, Youngsook L; Murn, Jernej; Ninova, Maria; Hubmann, Maria; Badeaux, Aimee I; Ang, Cheen Euong; Tenen, Danielle; Wesche, Daniel J; Abazova, Nadezhda; Hogue, Max; Tasdemir, Nilgun; Brumbaugh, Justin; Rathert, Philipp; Jude, Julian; Ferrari, Francesco; Blanco, Andres; Fellner, Michaela; Wenzel, Daniel; Zinner, Marietta; Vidal, Simon E; Bell, Oliver; Stadtfeld, Matthias; Chang, Howard Y.; Almouzni, Genevieve; Lowe, Scott W; Rinn, John; Wernig, Marius; Aravin, Alexei; Shi, Yang; Park, Peter; Penninger, Josef M; Zuber, Johannes; Hochedlinger, Konrad (2016)
      Cellular differentiation involves profound remodeling of chromatic landscapes, yet the mechanisms by which somatic cell identity is subsequently maintained remain incompletely understood. To further elucidate regulatory ...

    • Identification of proteins binding coding and non-coding human RNAs using protein microarrays 

      Siprashvili, Zurab; Webster, Dan E; Kretz, Markus; Johnston, Danielle; Rinn, John L; Chang, Howard Y; Khavari, Paul A (BioMed Central, 2012)
      Background: The regulation and function of mammalian RNAs has been increasingly appreciated to operate via RNA-protein interactions. With the recent discovery of thousands of novel human RNA molecules by high-throughput ...

    • Identifying Recent Adaptations in Large-Scale Genomic Data 

      Grossman, Shamai Aaron; Andersen, Kristian G; Shlyakhter, Ilya; Tabrizi, Shervin; Winnicki, Sarah M.; Yen, Angela; Park, Daniel J.; Griesemer, Dustin Shahab; Karlsson, Elinor Kathryn; Wong, Sunny H.; Cabili, Moran; Adegbola, Richard A.; Bamezai, Rameshwar N.K.; Hill, Adrian V.S.; Vannberg, Fredrik O.; Rinn, John L; Lander, Eric Steven; Schaffner, Stephen; Sabeti, Pardis Christine (Elsevier BV, 2013)
      Summary: Although several hundred regions of the human genome harbor signals of positive natural selection, few of the relevant adaptive traits and variants have been elucidated. Using full-genome sequence variation from ...

    • In vivo Ebola virus infection leads to a strong innate response in circulating immune cells 

      Caballero, Ignacio S.; Honko, Anna N.; Gire, Stephen K.; Winnicki, Sarah M.; Melé, Marta; Gerhardinger, Chiara; Lin, Aaron E.; Rinn, John L.; Sabeti, Pardis C.; Hensley, Lisa E.; Connor, John H. (BioMed Central, 2016)
      Background: Ebola virus is the causative agent of a severe syndrome in humans with a fatality rate that can approach 90 %. During infection, the host immune response is thought to become dysregulated, but the mechanisms ...

    • Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer 

      Du, Zhou; Sun, Tong; Hacisuleyman, Ezgi; Fei, Teng; Wang, Xiaodong; Brown, Myles; Rinn, John L.; Lee, Mary Gwo-Shu; Chen, Yiwen; Kantoff, Philip W.; Liu, X. Shirley (Nature Publishing Group, 2016)
      Mounting evidence suggests that long noncoding RNAs (lncRNAs) can function as microRNA sponges and compete for microRNA binding to protein-coding transcripts. However, the prevalence, functional significance and targets ...

    • Integrative Characterization of Human Long Non-Coding RNAs 

      Cabili, Nataly Moran (2014-06-06)
      Since its early discovery as a messenger, RNA has been shown to play a diverse set of regulatory, structural and even catalytic roles. The more recent understanding that the genome is pervasively transcribed stimulated the ...

    • Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage 

      Younger, Scott T.; Kenzelmann-Broz, Daniela; Jung, Heiyoun; Attardi, Laura D.; Rinn, John L. (Oxford University Press, 2015)
      The tumor suppressor p53 has been studied extensively as a direct transcriptional activator of protein-coding genes. Recent studies, however, have shed light on novel regulatory functions of p53 within noncoding regions ...

    • A Keystone for ncRNA 

      Hacisuleyman, Ezgi; Cabili, Moran N; Rinn, John L (BioMed Central, 2012)
      A report on the Keystone symposium 'Non-coding RNAs' held at Snowbird, Utah, USA, 31 March to 5 April 2012.

    • Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution 

      Cabili, Moran N; Dunagin, Margaret C; McClanahan, Patrick D; Biaesch, Andrew; Padovan-Merhar, Olivia; Regev, Aviv; Rinn, John L; Raj, Arjun (BioMed Central, 2015)
      Background: Long non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. In contrast to extensive genomic annotation of lncRNA transcripts, far fewer have been characterized for subcellular localization ...

    • The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan 

      Kotzin, Jonathan J.; Spencer, Sean Paul; McCright, Sam J.; Kumar, Dinesh B. Uthaya; Collet, Magalie A.; Mowel, Walter K.; Elliott, Ellen N.; Uyar, Asli; Makiya, Michelle A.; Dunagin, Margaret C.; Harman, Christian C.D.; Virtue, Anthony T.; Zhu, Stella; Bailis, Will; Stein, Judith; Hughes, Cynthia; Raj, Arjun; Wherry, E. John; Goff, Loyal; Klion, Amy D.; Rinn, John L; Williams, Adam; Flavell, Richard A.; Henao-Mejia, Jorge (Springer Nature, 2016)
      Neutrophils, eosinophils and “classical” monocytes collectively account for ~70% ofhuman blood leukocytes and are among the shortest-lived cells in the body. Precise regulation of the lifespan of these myeloid cells is ...

    • Long Noncoding RNAs Regulate Adipogenesis 

      Sun, Lei; Goff, Loyal Andrew; Trapnell, Cole; Alexander, Ryan Kendall; Lo, Kinyui Alice; Hacisuleyman, Ezgi; Sauvageau, Martin; Tazon-Vega, Barbara; Kelley, David Roy; Hendrickson, David Gillis; Yuan, Bingbing; Kellis, Manolis; Lodish, Harvey F.; Rinn, John L (Proceedings of the National Academy of Sciences, 2013)
      The prevalence of obesity has led to a surge of interest in understanding the detailed mechanisms underlying adipocyte development. Many protein-coding genes, mRNAs, and microRNAs have been implicated in adipocyte development, ...

    • Multiple knockout mouse models reveal lincRNAs are required for life and brain development 

      Sauvageau, Martin; Goff, Loyal A; Lodato, Simona; Bonev, Boyan; Groff, Abigail F; Gerhardinger, Chiara; Sanchez-Gomez, Diana B; Hacisuleyman, Ezgi; Li, Eric; Spence, Matthew; Liapis, Stephen C; Mallard, William; Morse, Michael; Swerdel, Mavis R; D’Ecclessis, Michael F; Moore, Jennifer C; Lai, Venus; Gong, Guochun; Yancopoulos, George D; Frendewey, David; Kellis, Manolis; Hart, Ronald P; Valenzuela, David M; Arlotta, Paola; Rinn, John L (eLife Sciences Publications, Ltd, 2013)
      Many studies are uncovering functional roles for long noncoding RNAs (lncRNAs), yet few have been tested for in vivo relevance through genetic ablation in animal models. To investigate the functional relevance of lncRNAs ...