UCSF RNA Journal Club

A newsletter announcing the next presenter for RNA Journal Club

Speaker from ThermoFisher

TBA
Date: 
October 25, 2017
Where: 
HSW 1057 at noon

John Gagnon

TBA
Date: 
October 18, 2017
Where: 
HSW 1057 at noon

Leonardo Ramos Ferreira

TBA
Date: 
October 11, 2017
Where: 
HSW 1057 at noon

Michael McManus

TBA
Date: 
October 4, 2017
Where: 
HSW 1057 at noon

Mary Ann Santos

Accelerating Discovery with CRISPR Editing
Learn how genomic engineering can help build your next breakthrough! Built on 20 years of industry-leading innovation, our comprehensive genome engineering portfolio can help you meet your research needs. Together with an overview of the entire genome engineering workflow, we will focus on how to utilize the newest technologies of the CRISPR/Cas9 system to accelerate your discovery research. * The various CRISPR-Cas9 formats available today and which is best for your specific application * Transfection optimization for efficient CRISPR-Cas9 delivery * Donor synthesis for knock-in experiments * The latest easy-to-use assays for detecting and enriching cells with edited genomes * How to troubleshoot your CRISPR experiments to achieve higher efficiencies with minimal off-target effects * CRISPR lentiviral and purified gRNA libraries for screening applications * Case study of a custom cell line engineering project (knock out) Don’t miss our discussion regarding CRISPRs. For more information about this event, please contact: Jonas Ruiz [email protected] or Mary Ann Santos [email protected]
Date: 
May 31, 2017
Where: 
HSW 1057 at noon

Maryia Barnett

Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9
Niu D1,2, Wei HJ3,4, Lin L5, George H1, Wang T1, Lee IH1, Zhao HY3, Wang Y6, Kan Y1, Shrock E7, Lesha E1, Wang G1, Luo Y5, Qing Y3,4, Jiao D3,4, Zhao H3,4, Zhou X6, Wang S8, Wei H6, Güell M1, Church GM1,7,9, Yang L10.
Science. 2017 Aug 10. pii: eaan4187. doi: 10.1126/science.aan4187. [Epub ahead of print]
eGenesis, Inc., Cambridge, MA 02139, USA. College of Animal Sciences, Zhejiang University, Hangzhou 310058, China. State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China. College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China. Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark. Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, 400038, P. R. China. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Research Institute of Shenzhen Jinxinnong Technology CO., LTD., Shenzhen 518106, China. Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA. eGenesis, Inc., Cambridge, MA 02139, USA. [email protected]
Xenotransplantation is a promising strategy to alleviate the shortage of organs for human transplantation. In addition to the concern on pig-to-human immunological compatibility, the risk of cross-species transmission of porcine endogenous retroviruses (PERVs) has impeded the clinical application of this approach. Earlier, we demonstrated the feasibility of inactivating PERV activity in an immortalized pig cell line. Here, we confirmed that PERVs infect human cells, and observed the horizontal transfer of PERVs among human cells. Using CRISPR-Cas9, we inactivated all the PERVs in a porcine primary cell line and generated PERV-inactivated pigs via somatic cell nuclear transfer. Our study highlighted the value of PERV inactivation to prevent cross-species viral transmission and demonstrated the successful production of PERV-inactivated animals to address the safety concern in clinical xenotransplantation.
Date: 
September 27, 2017
Where: 
HSW 1057 at noon

Kol Jia Yong

A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems
Kazlauskiene M, Kostiuk G, Venclovas Č, Tamulaitis G, Siksnys V.
Science. 2017 Aug 11;357(6351):605-609. doi: 10.1126/science.aao0100. Epub 2017 Jun 29.
August 11, 2017
Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania. Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania. [email protected] [email protected]
Type III CRISPR-Cas systems in prokaryotes provide immunity against invading nucleic acids through the coordinated degradation of transcriptionally active DNA and its transcripts by the Csm effector complex. The Cas10 subunit of the complex contains an HD nuclease domain that is responsible for DNA degradation and two Palm domains with elusive functions. In addition, Csm6, a ribonuclease that is not part of the complex, is also required to provide full immunity. We show here that target RNA binding by the Csm effector complex of Streptococcus thermophilus triggers Cas10 to synthesize cyclic oligoadenylates (cA n ; n = 2 to 6) by means of the Palm domains. Acting as signaling molecules, cyclic oligoadenylates bind Csm6 to activate its nonspecific RNA degradation. This cyclic oligoadenylate-based signaling pathway coordinates different components of CRISPR-Cas to prevent phage infection and propagation.
Date: 
September 20, 2017
Where: 
HSW 1057 at noon

Gabriel Eades

A heterochromatin-dependent transcription machinery drives piRNA expression
Peter Refsing Andersen, Laszlo Tirian, Milica Vunjak & Julius Brennecke.
Nature. 2017 Sep 7;549(7670):54-59. doi: 10.1038/nature23482. Epub 2017 Aug 23.
August 23, 2017
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria.
Nuclear small RNA pathways safeguard genome integrity by establishing transcription-repressing heterochromatin at transposable elements. This inevitably also targets the transposon-rich source loci of the small RNAs themselves. How small RNA source loci are efficiently transcribed while transposon promoters are potently silenced is not understood. Here we show that, in Drosophila, transcription of PIWI-interacting RNA (piRNA) clusters—small RNA source loci in animal gonads—is enforced through RNA polymerase II pre-initiation complex formation within repressive heterochromatin. This is accomplished through Moonshiner, a paralogue of a basal transcription factor IIA (TFIIA) subunit, which is recruited to piRNA clusters via the heterochromatin protein-1 variant Rhino. Moonshiner triggers transcription initiation within piRNA clusters by recruiting the TATA-box binding protein (TBP)-related factor TRF2, an animal TFIID core variant. Thus, transcription of heterochromatic small RNA source loci relies on direct recruitment of the core transcriptional machinery to DNA via histone marks rather than sequence motifs, a concept that we argue is a recurring theme in evolution.
Date: 
September 13, 2017
Where: 
HSW 1057 at noon

Theodore Roth

In Situ Capture of Chromatin Interactions by Biotinylated dCas9
Liu X1, Zhang Y1, Chen Y2, Li M3, Zhou F4, Li K1, Cao H1, Ni M1, Liu Y1, Gu Z1, Dickerson KE1, Xie S5, Hon GC5, Xuan Z2, Zhang MQ6, Shao Z3, Xu J7.
Cell. 2017 Aug 24;170(5):1028-1043.e19. doi: 10.1016/j.cell.2017.08.003.
August 24, 2017
Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA. Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Minister of Education, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China. Electronic address: [email protected] Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA; MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China. Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: [email protected]
Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here, we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated nuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single-copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally regulated super-enhancers reveals spatial features that causally control gene transcription. Thus, comprehensive and unbiased analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.
Date: 
September 6, 2017
Where: 
HSW 1057 at noon

Eleonora De Klerk

Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription
Werner MS1, Sullivan MA1,2, Shah RN1,2, Nadadur RD3, Grzybowski AT1, Galat V4, Moskowitz IP3, Ruthenburg AJ1,2.
Nat Struct Mol Biol. 2017 Jul;24(7):596-603. doi: 10.1038/nsmb.3424. Epub 2017 Jun 19.
July 1, 2017
Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA. Department of Pediatrics and Pathology, The University of Chicago, Chicago, Illinois, USA. Department of Pathology, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
We recently described a new class of long noncoding RNAs (lncRNAs) that are distinguished by especially tight chromatin association and whose presence is strongly correlated to expression of nearby genes. Here, we examine the cis-enhancer mechanism of this class of chromatin-enriched RNA (cheRNA) across multiple human cell lines. cheRNAs are largely cell type specific and provide the most reliable chromatin signature to predict cis-gene transcription in every human cell type examined. Targeted depletion of three cheRNAs decreases expression of their neighboring genes, indicating potential co-activator function, and single-molecule fluorescence in situ hybridization (smFISH) of one cheRNA-distal target gene pair suggests a spatial overlap consistent with a role in chromosome looping. Additionally, the cheRNA HIDALGO stimulates the fetal hemoglobin subunit gamma 1 (HBG1) gene during erythroid differentiation by promoting contacts to a downstream enhancer. Our results suggest that multiple cheRNAs activate proximal lineage-specific gene transcription.
Date: 
August 30, 2017
Where: 
HSW 1057 at noon