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Genes & Development

Edited By T. Grodzicker, Cold Spring Harbor Laboratory Press

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© 2020 • ISSN 0890-9369; Volume 34 includes full online access
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Genes & Development publishes high-quality research papers of broad general interest and biological significance in the areas of molecular biology, molecular genetics, and related fields. G&D publishes two research formats; Research papers and short Research Communications, in addition to Review Articles and Perspectives. G&D consistently ranks in the top 10 among primary research journals in all fields of science.
This journal is published in association with The Genetics Society.
Subscription to the print journal includes full access to the online edition (online-only subscriptions are available upon request).

 
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Genome Research

Edited By Hillary Sussman, Cold Spring Harbor Laboratory Press; Aravinda Chakravarti, Johns Hopkins School of Medicine; Richard Gibbs, Baylor College of Medicine; Eric Green, Bethesda, MD; Richard Myers, HudsonAlpha Institute for Biotechnology; William Pavan, Derwood, MD

Online Features: Internet edition – Genome Research Online at Stanford University Libraries' HighWire Press; Electronic supplementary material – auxiliary data available only via the journal's online edition

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© 2020 • ISSN: 1088-9051; Volume 30 includes full online access
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January - December 2020, 12 monthly issues
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In August 1995, Cold Spring Harbor Laboratory Press began publication of a new, monthly, international, peer-reviewed journal, Genome Research. The journal focuses on genome studies in all species, and presents research that provides or aids in genome-based analyses of biological processes. The journal represents a nexus point where genomic information, applications, and technology come together with biological information to create a more global understanding of all biological systems.

Among the research considered by the journal are novel reports on gene discovery, comparative genome analyses, evolution studies, informatics, genome structure and function, technological innovations and applications, statistical and mathematical methods, cutting-edge genetic and physical mapping and DNA sequencing, and other reports that present data where sequence information is used to address biological concerns.

New data in these areas are published as research papers in the form of articles and letters, or methods and resource reports that provide novel information on methodologies or resources that will be of interest to a broad readership. Complete data sets are presented electronically on the journal's web site where appropriate. The journal also provides review articles, perspectives, and Insight/Outlook articles, which presents commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context.

Subscription to the print journal includes full access to the online edition (online-only subscriptions are not available).

 
 

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Learning & Memory

Edited By John H. Byrne, University of Texas School of Medicine

Online Features: Internet edition – Learning & Memory Online at Stanford University Libraries' HighWire Press

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© 2020 • ISSN 1549-5485; Volume 27; includes full online access
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Learning & Memory is the journal of choice for interdisciplinary studies on synaptic plasticity, learning, and memory. Until now, there has been no one journal devoted to this area of study and no dominant journal that demands attention by serious workers in the area, regardless of specialty. Spanning molecules, cells, systems, and behavior, L&M considers research using approaches from cellular and molecular biology, genetics, biochemistry, computational neuroscience, neurophysiology, neuropharmacology, neuroanatomy, behavior, and cognition. Learning & Memory provides a forum for these investigations in the form of original research papers, review articles, and brief communications.

 
 

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CSH Perspectives in Medicine

Online Features: CSH Perspectives in Medicine – CSH Perspectives in Medicine at Stanford University Libraries' HighWire Press

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© 2020 • ISSN: 2157-1422; Volume 10 includes full online access
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cironek@cshl.edu.

January - December 2020, 12 monthly issues
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Cold Spring Harbor Perspectives in Medicine is a new online publication covering everything from the molecular and cellular bases of disease to translational medicine and new therapeutic strategies. Each issue offers reviews on different aspects of a variety of diseases and the tissues they affect. The contributions are written by experts in each field and commissioned as Subject Collections by a board of eminent scientists and physicians, all of whom are acknowledged to be key figures in their particular fields. These Subject Collections gradually accumulate articles as new issues of the journal are published and, when complete, each represents a comprehensive survey of the field it covers. Cold Spring Harbor Perspectives in Medicine is thus unmatched in its depth of coverage and represents an essential source where readers can find informed surveys and critical discussion of advances in molecular medicine.

Please visit www.perspectivesinmedicine.org for complete information about the journal.

Subject Coverage includes:

  • Addiction
  • Aging
  • Alzheimer Disease
  • Anemia
  • Antibiotic Resistance
  • Bacterial Pathogens
  • Bone Disease
  • Cancer
  • Cystic Fibrosis
  • Diabetes
  • Heart Disease
  • Hemoglobin
  • HIV
  • Influenza
  • Malaria
  • Multiple Sclerosis
  • Muscular Dystrophy
  • Parkinson's Disease
  • Prion Diseases
  • Skin Diseases
  • Schizophrenia
 
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CSH Perspectives in Biology

Online Features: CSH Perspectives in Biology – CSH Perspectives in Biology at Stanford University Libraries' HighWire Press

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© 2020 • ISSN: 1943-0264; Volume 12 includes full online access
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January - December 2020, 12 monthly issues
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A new online publication for the molecular life sciences

Cold Spring Harbor Perspectives in Biology provides the scientific community with comprehensive, systematic surveys of topics in the molecular life sciences where research is breaking new ground

In July 2009, Cold Spring Harbor Laboratory Press launched a new monthly journal, Cold Spring Harbor Perspectives in Biology, that provides comprehensive, systematically structured surveys of research in exciting areas of molecular and cellular biology, genetics, developmental biology, neuroscience, cancer biology, and molecular pathology.

For decades, Cold Spring Harbor Laboratory has complemented its groundbreaking research with publication of a variety of highly prestigious titles written and edited by leading scientists. These include the journals Genes & Development and Genome Research, the bible of research methods, Molecular Cloning, online teaching resources, and numerous other laboratory manuals, monographs, handbooks, journals, and textbooks.

Cold Spring Harbor Perspectives in Biology (http://www.cshperspectives.org; ISSN 1943-0264) is the latest, and perhaps most ambitious, addition to this stable. Its depth of coverage is unmatched, spanning the entire spectrum of the molecular life sciences and therefore providing an essential resource for all areas of bioscience research.

According to the journal's Executive Editor, Richard Sever, who has worked on traditional review journals including the Current Opinion and Trends titles, Cold Spring Harbor Perspectives in Biology has a new and unique approach. "There are many review articles published each year, but they're usually on one particular aspect of one particular field," he says. "CSH Perspectives is different. We cover subjects by asking experts to consider how best to structure a comprehensive survey of their field, and then commission articles from all the key figures in that field. And we cover everything in bioscience from Alzheimer's to plant biology."

CSH Perspectives articles are all commissioned as �collections� by a board of eminent academic editors and gradually accumulate online at the journal's website each month as they are accepted and published. The debut issue features articles commissioned by Elaine Fuchs, Michael Karin, W. James Nelson, and Peter Lawrence and includes contributions from Nobel laureate David Baltimore, molecular motor expert Nobutaka Hirokawa, and developmental biologist Jim Smith. These set the stage for subject collections on symmetry breaking, morphogen gradients, cell junctions, and the immune signaling molecule NF-kB. Next in the pipeline are articles on the origin of life, the p53-family of tumor suppressors, the nucleus, and immune tolerance.

The new publication is produced online in partnership with Stanford University Library's HighWire Press, taking advantage of their new H20 platform. The state-of-the-art website includes HTML and PDF views, high-resolution artwork, and video material, along with a host of novel features such as author updates, commenting options, and Twitter-powered news feeds.

 
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CSH Protocols

Edited By Richard Sever, Cold Spring Harbor Laboratory Press

Online Features: Internet edition – Cold Spring Harbor Protocols at Stanford University Libraries' HighWire Press

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© 2020 • ISSN: 1559-6095; Volume 15; includes full online access
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January - December 2020, 12 monthly issues
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Description

  • The online source of trusted techniques in molecular and cellular biology
  • Contains new and classic protocols presented step-by-step with recipes and troubleshooting
  • Frequently updated and annotated
  • Interactive, customizable, and fully searchable

The development of CSH Protocols is a response to requests from scientists for authoritative information about techniques with a broad editorial scope, delivered through a state-of-the-art online interface. At this site, you will find methods from Molecular Cloning along with selected protocols from many of our best-selling manuals, such as Cells and Antibodies, as well as protocols from Cold Spring Harbor's renowned on-site courses. In addition, you will discover new cutting-edge protocols submitted by and commissioned from laboratories worldwide. A peer-reviewed online journal, CSH Protocols is updated monthly.

Features include:
  • Step-by-step, uniformly structured formats for ease of use and printing, with clearly linked materials, cautions, recipes, and troubleshooting
  • Customizable, topic-based e-mail alerts for the latest updates in a particular field
  • Personal folders for storing favorite protocols and searches
  • Navigation tools including a specifically designed taxonomy for browsing and a variety of full-text search options
  • A kit search tool for fast access to time-saving resources
  • An online manuscript submission system for authors to contribute new protocols

CSH Protocols — More Than Just Methods.

Visit www.cshprotocols.org for more details on features, subscriptions, and manuscript submission.

  • Available exclusively via institutional site license
  • ISSN 1559-6095 / online, monthly

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RNA

Edited By Timothy W. Nilsen, Editor-in-Chief, Case Western Reserve University; Thomas R. Cech, Howard Hughes Medical Institute; David Engelke, University of Michigan; Eric Westhof, CNRS Strasbourg; Marvin Wickens, University of Wisconsin

Online Features: Internet edition – RNA Online at Stanford University Libraries' HighWire Press

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© 2020 • ISSN 1355-8382; Volume 26; includes full online access.
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(Published by CSHL Press for The RNA Society)
January - December 2020, 12 monthly issues
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RNA, the publication of the RNA Society, publishes high quality research papers that provide significant new insight into any area of RNA biology, including molecular biology, cell biology, biochemistry, bioinformatics, genetics and evolution. RNA publishes two research formats, articles and short reports. In addition, the journal publishes novel methodologies, reviews and perspectives. RNA provides a unique resource to all members of the RNA community and those that wish to keep abreast of this quickly moving area.

 
 

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Hepatitis C Virus: The Story of a Scientific and Therapeutic Revolution

Hepatitis C is a liver disease caused by infection with the hepatitis C virus (HCV), a bloodborne pathogen. In some people, an immune response will clear the infection; however, in most, the infection becomes chronic and treatment with antiviral medication is necessary to prevent serious liver damage and cancer. The eradication of HCV will require improved access to diagnosis and treatment, an enhanced understanding of virus–host interactions, and the development of an effective vaccine.

Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Medicine examines all aspects of the biology of HCV, the pathological consequences of infection, the current standard of hepatitis C treatment, and ongoing efforts to control the disease. Contributors discuss the structural and biochemical properties of HCV, the molecular details of its life cycle, and how it promotes liver disease by perturbing host cell signaling pathways. They likewise examine the innate and adaptive immune responses elicited by HCV and why those responses often fail to clear the infection. Direct-acting antiviral regimens to treat infected patients, the impacts of those treatments on hepatitis C epidemiology, and obstacles to HCV elimination (e.g., vaccine development) are also covered.

This volume includes additional perspectives on the discovery of HCV, historical milestones in HCV research, and animal and cell culture models of HCV infection. It is an essential reference for virologists, immunologists, and all clinical and laboratory investigators interested in eliminating HCV as a public health threat.

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© 2020 • 298 pages, illustrated (37 color and 2 B&W), index
Hardcover • $75.00 • ISBN 978-1-621823-19-3


 

Description

Hepatitis C is a liver disease caused by infection with the hepatitis C virus (HCV), a bloodborne pathogen. In some people, an immune response will clear the infection; however, in most, the infection becomes chronic and treatment with antiviral medication is necessary to prevent serious liver damage and cancer. The eradication of HCV will require improved access to diagnosis and treatment, an enhanced understanding of virus–host interactions, and the development of an effective vaccine.

Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Medicine examines all aspects of the biology of HCV, the pathological consequences of infection, the current standard of hepatitis C treatment, and ongoing efforts to control the disease. Contributors discuss the structural and biochemical properties of HCV, the molecular details of its life cycle, and how it promotes liver disease by perturbing host cell signaling pathways. They likewise examine the innate and adaptive immune responses elicited by HCV and why those responses often fail to clear the infection. Direct-acting antiviral regimens to treat infected patients, the impacts of those treatments on hepatitis C epidemiology, and obstacles to HCV elimination (e.g., vaccine development) are also covered.

This volume includes additional perspectives on the discovery of HCV, historical milestones in HCV research, and animal and cell culture models of HCV infection. It is an essential reference for virologists, immunologists, and all clinical and laboratory investigators interested in eliminating HCV as a public health threat.

 
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Contents

Preface
Hepatitis C Virus: 30 Years after Its Discovery
Michael Houghton
Hepatitis C Virus Structure: Defined by What It Is Not
Altaira D. Dearborn and Joseph Marcotrigiano
Cell Culture Systems of HCV Using JFH-1 and Other Strains
Takaji Wakita
Animal Models of Hepatitis C Virus Infection
Alexander Ploss and Amit Kapoor
Hepatitis C Virus Entry: Protein Interactions and Fusion Determinants Governing Productive Hepatocyte Invasion
Gisa Gerold, Rebecca Moeller, and Thomas Pietschmann
Hepatitis C Virus Replication
Keisuke Tabata, Christopher J. Neufeldt, and Ralf Bartenschlager
HCVAssembly and Egress via Modifications in Host Lipid Metabolic Systems
Kunitada Shimotohno
Rewiring Host Signaling: Hepatitis C Virus in Liver Pathogenesis
Alessia Virzì, Armando Andres Roca Suarez, Thomas F. Baumert, and Joachim Lupberger
Innate Immunity in Hepatitis C Virus Infection
Johannes Schwerk, Amina Negash, Ram Savan, and Michael Gale, Jr.
Control of HCV Infection by Natural Killer Cells and Macrophages
Hugo R. Rosen and Lucy Golden-Mason
T-Cell Immunity against the Hepatitis C Virus: A Persistent Research Priority in an Era of Highly Effective Therapy
Stephanie Smith, Jonathan R. Honegger, and Christopher Walker
Antibody Responses in Hepatitis C Infection
Mansun Law
Interferon-Free Hepatitis C Virus Therapy
Jean-Michel Pawlotsky
Hepatitis C Virus Epidemiology and the Impact of Interferon-Free Hepatitis C Virus Therapy
Jeffrey V. Lazarus, Elena Roel, and Ahmed M. Elsharkawy
Natural History of Hepatic and Extrahepatic Hepatitis C Virus Diseases and Impact of Interferon-Free HCV Therapy
Francesco Negro
The Elimination of Hepatitis C as a Public Health Threat
Margaret Hellard, Sophia E. Schroeder, Alisa Pedrana, Joseph Doyle, and Campbell Aitken
Challenges and Promise of a Hepatitis C Virus Vaccine
Andrea L. Cox
Index
 

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Hepatitis C Virus: The Story of a Scientific and Therapeutic Revolution


Subject Area(s):  Infectious DiseasesHuman Biology and DiseaseDiseasesViruses

Edited by Arash Grakoui, Emory University; Jean-Michel Pawlotsky, Hopital Henri Mondor / Universite Paris Est; Glenn Randall, University of Chicago

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Preface
Hepatitis C Virus: 30 Years after Its Discovery
Index


Due July 2020 • 298 pages, illustrated (37 color and 2 B&W), index
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ISBN  978-1-621823-19-3
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  •     Description    
  •     Contents    

Description

Hepatitis C is a liver disease caused by infection with the hepatitis C virus (HCV), a bloodborne pathogen. In some people, an immune response will clear the infection; however, in most, the infection becomes chronic and treatment with antiviral medication is necessary to prevent serious liver damage and cancer. The eradication of HCV will require improved access to diagnosis and treatment, an enhanced understanding of virus–host interactions, and the development of an effective vaccine.

Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Medicine examines all aspects of the biology of HCV, the pathological consequences of infection, the current standard of hepatitis C treatment, and ongoing efforts to control the disease. Contributors discuss the structural and biochemical properties of HCV, the molecular details of its life cycle, and how it promotes liver disease by perturbing host cell signaling pathways. They likewise examine the innate and adaptive immune responses elicited by HCV and why those responses often fail to clear the infection. Direct-acting antiviral regimens to treat infected patients, the impacts of those treatments on hepatitis C epidemiology, and obstacles to HCV elimination (e.g., vaccine development) are also covered.

This volume includes additional perspectives on the discovery of HCV, historical milestones in HCV research, and animal and cell culture models of HCV infection. It is an essential reference for virologists, immunologists, and all clinical and laboratory investigators interested in eliminating HCV as a public health threat.

Contents

Preface
Hepatitis C Virus: 30 Years after Its Discovery
Michael Houghton
Hepatitis C Virus Structure: Defined by What It Is Not
Altaira D. Dearborn and Joseph Marcotrigiano
Cell Culture Systems of HCV Using JFH-1 and Other Strains
Takaji Wakita
Animal Models of Hepatitis C Virus Infection
Alexander Ploss and Amit Kapoor
Hepatitis C Virus Entry: Protein Interactions and Fusion Determinants Governing Productive Hepatocyte Invasion
Gisa Gerold, Rebecca Moeller, and Thomas Pietschmann
Hepatitis C Virus Replication
Keisuke Tabata, Christopher J. Neufeldt, and Ralf Bartenschlager
HCVAssembly and Egress via Modifications in Host Lipid Metabolic Systems
Kunitada Shimotohno
Rewiring Host Signaling: Hepatitis C Virus in Liver Pathogenesis
Alessia Virzì, Armando Andres Roca Suarez, Thomas F. Baumert, and Joachim Lupberger
Innate Immunity in Hepatitis C Virus Infection
Johannes Schwerk, Amina Negash, Ram Savan, and Michael Gale, Jr.
Control of HCV Infection by Natural Killer Cells and Macrophages
Hugo R. Rosen and Lucy Golden-Mason
T-Cell Immunity against the Hepatitis C Virus: A Persistent Research Priority in an Era of Highly Effective Therapy
Stephanie Smith, Jonathan R. Honegger, and Christopher Walker
Antibody Responses in Hepatitis C Infection
Mansun Law
Interferon-Free Hepatitis C Virus Therapy
Jean-Michel Pawlotsky
Hepatitis C Virus Epidemiology and the Impact of Interferon-Free Hepatitis C Virus Therapy
Jeffrey V. Lazarus, Elena Roel, and Ahmed M. Elsharkawy
Natural History of Hepatic and Extrahepatic Hepatitis C Virus Diseases and Impact of Interferon-Free HCV Therapy
Francesco Negro
The Elimination of Hepatitis C as a Public Health Threat
Margaret Hellard, Sophia E. Schroeder, Alisa Pedrana, Joseph Doyle, and Campbell Aitken
Challenges and Promise of a Hepatitis C Virus Vaccine
Andrea L. Cox
Index
   

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RNA Control and Regulation

(Cold Spring Harbor Symposia on Quantitative Biology LXXXIV)

Subject Area(s):  BiotechnologyMolecular BiologyGeneticsBiochemistry

Edited by Terri Grodzicker, Cold Spring Harbor Laboratory; David Stewart, Cold Spring Harbor Laboratory; Bruce Stillman, Cold Spring Harbor Laboratory

Due August 2020 • Pages TBD, illustrated, index
Paperback • $89 71.20
ISBN  978-1-621823-92-6
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  •     Contents    

Description

Previous Cold Spring Harbor Symposia have addressed many different aspects of RNA biology such as Mechanisms of Transcription (1998), The Ribosome (2001), Epigenetics (2004) and Regulatory RNAs (2006). The 84th Cold Spring Harbor Symposium focused on RNA Control & Regulation and provided a current synthesis of the enormous progress in our understanding of RNA’s influence on cells and organisms and how, when aberrant, its effects may contribute to the progression of disease. It is rare to find such a wide-ranging perspective on this topic in one volume and this collection of papers will be valuable to investigators in many fields. The topics covered at the meeting included: RNA-Based Structures; RNA Modifications; Nuclear Localization of RNA; Quality Control & Editing; RNA & Gene Regulation; Cotranscriptional Splicing; Intron/Exon Boundaries; Alternative Polyadenylation; Transposon Control; Small Noncoding RNAs; Long Noncoding RNAs; RNA & Development; Membrane-Less Organelles; Phase Separation; RNA-Based Diseases; and Novel RNA Functions. Numerous speakers participated in interviews during the course of the Symposium week and this volume includes transcripts of those discussions and the Dorcas Cummings lecture, for the general public, which was given by Dr. Jennifer Doudna.

Contents

Preliminary
INTRODUCTION
RNP Granules in Health and Disease
Roy Parker
3′UTRs Regulate Protein Functions by Providing a Nurturing Niche during Protein Synthesis
Christine Mayr
GLOBAL ANALYSES AND STRUCTURES
Zipcode Binding Protein 1 (ZBP1; IGF2BP1): A Model for Sequence Specific RNA Regulation
Jeetayu Biswas, Leti Nunez, Sulagna Das, Young J. Yoon, Carolina Eliscovich, and Robert H. Singer
Coordination of RNA Processing Events In Vivo
Karla M. Neugebauer
The Intrinsic Structure of poly(A) RNA Determines the Specificity of Deadenylation
Lori A. Passmore
Genome Regulation by Long Noncoding RNAs
Furqan M. Fazal, Howard Y. Chang
REGULATION OF RNA FUNCTIONS
The THO Complex as a Paradigm for the Prevention of co-Transcriptional R-Loops
Rosa Luna, Ana G. Rondón, Carmen Pérez-Calero, Irene Salas-Armenteros, and Andrés Aguilera
LSM2-8 and XRN-2 Contribute to the Silencing of H3K27me3-Marked Genes through Targeted RNA Decay
Susan M. Gasser
Telescripting⎯U1 snRNP Suppression of Premature Transcription Termination as a New Layer of Gene Regulation
Gideon Dreyfuss
Nonsense-mediated mRNA Decay in Health and Disease
Lynn E. Maquat
GENE REGULATION
Mechanistic Dissection of RNA Binding Proteins in Regulated Gene Expression at Chromatin Levels
Jia-Yu Chen, Do-Hwan Lim, and Xiang-Dong Fu
Linking RNA Processing and Function
Run-Wen Yao, Chu-Xiao Liu, and Ling-Ling Chen
Attenuation of Eukaryotic Protein-Coding Gene Expression via Premature Transcription Termination
Deirdre C. Tatomer and Jeremy E. Wilusz
RNA AND DISEASE
Functional and Mechanistic Interplay of Host and Viral Alternative Splicing Regulation during Influenza Infection
Matthew G. Thompson and Kristen W. Lynch
Cell-specific RNA CLIP
Robert B. Darnell
SMALL RNAs AND DEFENSE SYSTEMS
How Complementary Targets Expose the MicroRNA 3′ End for Tailing and Trimming during Target-Directed MicroRNA Degradation
Paulina Pawlica, Jessica Sheu-Gruttadauria, Ian J. MacRae, and Joan A. Steitz
Dicer's Helicase Domain: A Meeting Place for Regulatory Proteins
Sarah R. Hansen, Adedeji M. Aderounmu, Helen M. Donelick, and Brenda L. Bass
Molecular and Structural Basis of the Interaction of Gtsf1/arx with tRNA in the piRNA Pathway
Leemor Joshua-Tor
Mechanisms of RNA Channeling from DNA Transcription to Argonaute Loading in the siRNA-directed DNA Methylation
Craig S. Pikaard
DEVELOPMENTAL REGULATION
Transposable Elements in Early Mammalian Development-Do They Burst?
Maria-Elena Torres-Padilla
CONDENSATES AND PHASE SEPARATION
Regulation of Heterochromatin Condensates by RNA and DNA
G.J. Narlikar
Architectural RNAs for Membraneless Nuclear Body Formation
Tomohiro Yamazaki, Shinichi Nakagawa, and Tetsuro Hirose
RNA Organization within Phase Transitioned Germ Granules
Ruth Lehmann
CHROMATIN AND RNA
The Chromosomal Impact of small RNAs
Robert A. Martienssen
Molecular Mechanisms of poly(A) Tail Length Regulation
Elena Conti
Long Noncoding RNAs in Development and Regeneration of the Neural Lineage
Hadas Nezroni, Rotem Ben Tov Perry, and Igor Ulitsky
SUMMARY Gideon Dreyfuss
Index
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