Faculty Opinions recommendation of Long-range chromatin regulatory interactions in vivo.

Abstract The gene and cell therapy fields are advancing rapidly, with a potential to treat and cure a wide range of diseases, and lentivirus-based gene transfer agents are the vector of choice for many investigators. Early cases of insertional mutagenesis caused by gammaretroviral vectors highlighted that integration site (IS) analysis was a major safety and quality control checkpoint for lentiviral applications. The methods established to detect lentiviral integrations using next-generation sequencing (NGS) are limited by short read length, inadvertent PCR bias, low yield, or lengthy protocols. Here, we describe a new method to sequence IS using Amplification-free Integration Site sequencing (AFIS-Seq). AFIS-Seq is based on amplification-free, Cas9-mediated enrichment of high-molecular-weight chromosomal DNA suitable for long-range Nanopore MinION sequencing. This accessible and low-cost approach generates long reads enabling IS mapping with high certainty within a single day. We demonstrate proof-of-concept by mapping IS of lentiviral vectors in a variety of cell models and report up to 1600-fold enrichment of the signal. This method can be further extended to sequencing of Cas9-mediated integration of genes and to in vivo analysis of IS. AFIS-Seq uses long-read sequencing to facilitate safety evaluation of preclinical lentiviral vector gene therapies by providing IS analysis with improved confidence.

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FAST MONITORING OF LONG-RANGE ORDER IN THE ENSEMBLE OF COLLAGEN DOMAINS IN THE ACHILLES TENDONS AND HUMAN KNEES IN VIVO

Molekulyarnaya Meditsina (Molecular medicine) ◽

10.29296/24999490-2019-03-10 ◽

2019 ◽

Vol 17 (3) ◽

Author(s):

Kristina Zubow ◽

Anatolij Zubow ◽

Viktor Zubow

Keyword(s):

Long Range ◽

Range Order ◽

Long Range Order

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Long-Range Energy Continua and the Coordination of Multienzyme Sequences in Vivo

Organized Multienzyme Systems: Catalytic Properties ◽

10.1016/b978-0-12-744040-8.50014-1 ◽

1985 ◽

pp. 419-447 ◽

Cited By ~ 4

Author(s):

G. Rickey Welch ◽

Michael N. Berry

Keyword(s):

Long Range

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In vivo non-invasive imaging of the adult zebrafish brain with a 1325 nm long range spectral-domain optical coherence tomography system

TENCON 2015 - 2015 IEEE Region 10 Conference ◽

10.1109/tencon.2015.7372887 ◽

2015 ◽

Author(s):

Jian Zhang ◽

Zhen Yuan

Keyword(s):

Optical Coherence Tomography ◽

Long Range ◽

Spectral Domain ◽

Optical Coherence ◽

Adult Zebrafish ◽

Zebrafish Brain ◽

Optical Coherence Tomography System ◽

Non Invasive ◽

Tomography System

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Long-Range Transcriptional Control of theIl2Gene by an Intergenic Enhancer

Molecular and Cellular Biology ◽

10.1128/mcb.00592-15 ◽

2015 ◽

Vol 35 (22) ◽

pp. 3880-3891 ◽

Cited By ~ 6

Author(s):

Parul Mehra ◽

Andrew D. Wells

Keyword(s):

Autoimmune Disease ◽

Long Range ◽

Transcriptional Control ◽

Regulatory Element ◽

Interleukin 2 ◽

Regulatory Region ◽

Dependent Manner ◽

Regulatory Architecture

Interleukin-2 (IL-2) is a potent cytokine with roles in both immunity and tolerance. Genetic studies in humans and mice demonstrate a role forIl2in autoimmune disease susceptibility, and for decades the proximalIl2upstream regulatory region has served as a paradigm of tissue-specific, inducible gene regulation. In this study, we have identified a novel long-range enhancer of theIl2gene located 83 kb upstream of the transcription start site. This element can potently enhanceIl2transcription in recombinant reporter assaysin vitro, and the native region undergoes chromatin remodeling, transcribes a bidirectional enhancer RNA, and loops to physically interact with theIl2genein vivoin a CD28-dependent manner in CD4+T cells. Thiscisregulatory element is evolutionarily conserved and is situated near a human single-nucleotide polymorphism (SNP) associated with multiple autoimmune disorders. These results indicate that the regulatory architecture of theIl2locus is more complex than previously appreciated and suggest a novel molecular basis for the genetic association ofIl2polymorphism with autoimmune disease.

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Hippocampal hub neurons maintain distinct connectivity throughout their lifetime

Nature Communications ◽

10.1038/s41467-020-18432-6 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 2

Author(s):

Marco Bocchio ◽

Claire Gouny ◽

David Angulo-Garcia ◽

Tom Toulat ◽

Thomas Tressard ◽

...

Keyword(s):

Functional Connectivity ◽

Long Range ◽

Calcium Imaging ◽

Ex Vivo ◽

Adult Brain ◽

Cell Assemblies ◽

Population Synchrony ◽

Neurochemical Analysis ◽

In Vivo Calcium Imaging

Abstract The temporal embryonic origins of cortical GABA neurons are critical for their specialization. In the neonatal hippocampus, GABA cells born the earliest (ebGABAs) operate as ‘hubs’ by orchestrating population synchrony. However, their adult fate remains largely unknown. To fill this gap, we have examined CA1 ebGABAs using a combination of electrophysiology, neurochemical analysis, optogenetic connectivity mapping as well as ex vivo and in vivo calcium imaging. We show that CA1 ebGABAs not only operate as hubs during development, but also maintain distinct morpho-physiological and connectivity profiles, including a bias for long-range targets and local excitatory inputs. In vivo, ebGABAs are activated during locomotion, correlate with CA1 cell assemblies and display high functional connectivity. Hence, ebGABAs are specified from birth to ensure unique functions throughout their lifetime. In the adult brain, this may take the form of a long-range hub role through the coordination of cell assemblies across distant regions.

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