Feng Zhang
@zhangf
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Researcher at Broad Institute and McGovern Institute at MIT.
Cambridge, MA
Joined April 2015
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CRISPR technologies are powerful gene editing tools because they are programmable. We are excited to describe 3 new programmable systems, IscB, IsrB, and TnpB, some of the most abundant genes on the planet, with potential for gene editing.
@ScienceMagazine
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We are excited to share STOPCovid, an inexpensive, one-step, & sensitive
#COVID
-19 detection protocol developed with
@omarabudayyeh
&
@jgooten
. This revamped assay was streamlined with the future goal of developing an in-home test for COVID-19. 1/X
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We are really excited to share our work on a new modular RNA delivery technology called SEND, built from endogenous components found in the mammalian genome.
@ScienceMagazine
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Our genomes are littered with *junk* DNA known as LINE retrotransposons, which are powerful enzymes that can insert DNA into the genome. We are excited to report the structure of the LINE family member R2 and ways to engineer it for programmable gene insertion. Congratulations to
How do LINE family retrotransposons jump around?
Can we reprogram retrotransposons?
What does this have to do with Rum and Raisin?
Answers here and below!
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Extracting RNA from patient swab samples has been a bottleneck for
#COVID19
#coronavirus
testing. See here for a simple 5-min protocol from swab to RT-qPCR.
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Today we are sharing a research protocol for SHERLOCK-based COVID-19
#coronavirus
detection, and hope it will help others who are working to combat the outbreak. We will continue to update this as we make further progress:
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Thrilled to announce our latest exploration of CRISPR! By developing an advanced algorithm, we’ve analyzed 8 terabases of microbial data, leading to the discovery of over 200 novel CRISPR systems. Kudos to
@altaetran
and
@soumya_kannan12
for their exceptional work! Details in the
Our latest work exploring ultra rare CRISPR systems with new big data algorithms has been published by
@ScienceMagazine
!
@zhangf
@soumya_kannan12
. This thread will unwrap how we found needles in a haystack of metagenomes. Let's dive in! (1/8)
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CRISPR systems are quite diverse, including some, like CRISPR-Cas13, which target RNA.
@soumya_kannan12
&
@altaetran
found tiny versions of Cas13b (Cas13bt) that can be used to create RNA editors small enough to fit into a single AAV for in vivo delivery.
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Very cool - rejuvenation of the immune system!
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Did you know there are lots of similarities between the innate immune systems of animals/plants and the phage defense systems in bacteria? Check out our new study by the amazing trio Alex (Linyi) Gao,
@maxewilkinson
, and
@thestrecker
. Congratulations! .
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#CRISPR2022
begins today! Excited for all of the great discussions and learnings this week.
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I’m so incredibly excited and inspired to see
@eric_lander
(and
@FrancesArnold
and
@maria_zuber
) shaping the scientific future of our country in their new roles in
@JoeBiden
's science team! It gives me even more hope for our future!
This team will help our administration confront some of the biggest crises and challenges of our time, from climate change and the impact of technology on society to pandemics, racial inequity, and the current historic economic downturn.
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Thank you, Dr. Fauci.
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Excited to share STOPCovid.v2 for
#COVID19
diagnostics. Grateful for collaborators who helped make this happen!
@JuliaJoung
@LadhaAlim
@jgooten
@omarabudayyeh
KeithJerome
@GreningerLab
NamGyunKim
@UWVirology
@AnnWoolleyMD
DebHung
@brucedwalkermd
@DrJLi
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Congratulations and thank you to
@rahulkdhanda
and the entire
@Sherlock_Bio
team for achieving this huge milestone for the
#CRISPR
field. Proud of all teams working hard to fight this pandemic!
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A beautiful bridging (pun intended) of basic science and technology!
Just shared at
@KeystoneSymp
a new
@ArcInstitute
discovery of the bridge RNA recombinase mechanism: a new class of natural RNA-guided systems that retains the key property of programmability from RNAi and CRISPR while enabling large-scale genome design beyond RNA and DNA cuts
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We are pleased to share a follow-up story to our study of CRISPR-associated transposases (CAST) led by Makoto Saito,
@LadhaAlim
,
@thestrecker
, and Guilhem Faure: . 1/5
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The Biden Era Begins
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Inspiring visit at the
@arcinstitute
today with
@pdhsu
&
@SKonermann
. Thoughtful vision, exciting science, and amazing potential.
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1/N Excited to unveil Tn7 transposon target selectors study! What defines the target specificity of Tn7-like Tn to spread to MGEs & integrate back into bacterial genomes?
#transposons
#Tn7
#CAST
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This is really exciting!
Therapeutic mRNA for heart failure?!
Our own Joel Rurik (
@DevBioAcademic
) teamed up with
@WeissmanLab
to make CAR T cells entirely in the body to treat heart disease.
Published today on the cover of Science!
@CAMBUpenn
@PennBGS
@ScienceMagazine
1/6
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Excited to announce HowWeFeel, an open platform for helping us fight the pandemic. Grateful for collaboration w/
@8en
@XihongLin
@kinggary
@ophirshalem
@GreeneScientist
@bitdrift
@rpjb
and many other great colleagues. Visit .
#COVID19Pandemic
#coronavirus
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Had a blast diving deep into discussions on leadership, community, culture, and scientific vision at the
@broadinstitute
's annual faculty retreat. Also, that engineering challenge was a fun twist! 🧪
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Congratulations
@nevillesanjana
! Elegant and very timely!
As promised, here’s an overview of our study to find host factors required for SARS-CoV-2 infection in human cells. We use a genome-wide CRISPR screen to identify genes (& key mechanisms) that might be therapeutically targetable to prevent viral infection.
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Registrations are open for
#CRISPR2022
, at
@MIT
06/12/22-06/16/22. Featuring keynote by
@eugene_koonin
and many other exciting speakers. . Register today!
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Enabling testing at home and in low-resource settings requires that we can’t be reliant on complex instrumentation.
#STOPCovid
can be used with a sous-vide cooker (<$40). 3/X
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8/ This was led by
@altaetran
&
@soumya_kannan12
, and with EDemircioglu,
@rachel_oshiro
, SNety,
@GCACTAATTGAGAAC
, MDlakic,
@Ivan_Bilinski
, KMakarova, RMacrae,
@eugene_koonin
. We are excited to continue exploring nature’s diversity and advancing programmable therapeutics.
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Congratulations
@JuliaJoung
and team on a beautiful study utilizing genome-scale CRISPR activation screening to discover drivers for resistance to T-cell killing, with implications for immunotherapy for cancer.
Excited to share the latest work from my PhD! We performed the first CRISPR activation screen to identify genes that drive solid tumor resistance to T cell-mediated cytotoxicity. A thread 1/X
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We have some LwCas13 protein to share for research purposes with thanks to
@NEBiolabs
for providing a batch for us to share. Please fill out the form to request some for your project. Limited availability.
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We have an open position for a 🧬 Molecular Biologist/Biochemist/Structural Biologist. We look forward to hearing from you!
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Thank you
@eugene_koonin
for your science and even more importantly for your humanity. I’m so honored to have you as my colleague and friend.
Dr. Eugene Koonin, a member of National Academy of Sciences of the USA and of Russian Academy of Sciences, wrote this open letter today to the President of RAS Prof. Alexander Sergeev demanding that RAS issues an official anti-war statement in 48h, otherwise he resigns from RAS.
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8/ Last but not least, this was led by postdoc
@michael_s_segel
and grad student
@blake_lash
, and great collaborators JSong
@catherinecliu
(not pic'd
@xinjin
@LadhaAlim
SLMekhedov RMacrae
@eugene_koonin
). We are excited to continue developing SEND into a therapy to help patients.
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We are making a limited number of research-use-only
#STOPCovid
reagents available for free to the research community. Updates to the protocol and data will be added to our website .
Reagent request form:
6/6
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#STOPCovid
requires no sample extraction, can be performed using a single mastermix, and uses a paper strip to display results.
#STOPCovid
can detect down to 100 copies of SARS-Cov-2 RNA from patient samples. 2/X
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1/ Inspired by the machinery used by endosymbiotic bacteria to deliver protein payloads to their host animals’ cells, we sought to engineer these systems, called contractile injection systems (CISs), for delivery to human cells.
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Congratulations
@soumya_kannan12
and
@altaetran
!
The February issue is live
Our cover features a rendering of the predicted structure of an RNA editor based on the compact Cas13bt enzyme presented by Kannan et al.
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Please join us in Cambridge, MA for the 7th annual Genome Engineering Workshop May 19 & 20th, 2019.
The theme this year is CRISPR in vivo.
Look forward to seeing you there!
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Congratulations to the 2024 class of
@Regeneron
#sciencetalentsearch
finalists - inspirations and hopes for the future. Keep persevering, keep shining!
@Society4Science
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Super proud of the
#STOPCovid
team,
@JuliaJoung
,
@LadhaAlim
,
@omarabudayyeh
,
@jgooten
, MSegel, MSaito, RMacrae, and EBlackwell who have worked tirelessly for achieving this advance. We are charging forward to develop this into a turn-key solution for at-home testing. 4/X
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Check out the resource provided by Mammoth. Glad that scientists are working together and sharing openly.
#coronavirus
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Congratulations to
@thestrecker
, Esra Dimircioglu,
@_David_Li
,
@GuilhemFaure
, and co on another tour de force study in
@ScienceMagazine
! Elegant biology & beautiful integration of diverse techniques. Still so much more to explore! See David’s tweets for details.
Excited to see our work in the ZLab
@zhangf
on the protease Csx29 out! Led by the amazing
@thestrecker
with beautiful structures driven by Esra Dimircioglu, we show that Csx29 complexed with CRISPR protein Cas7-11 (aka gRAMP) is an RNA-triggered protease.
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5/ IscB can be engineered to edit genomes in human cells. The small size of IscB (~30% the size of Cas9) makes it an ideal candidate for in vivo genome editing technologies.
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Many “thank you” to my entire lab and lab alum for putting together a phenomenal GE7.0 workshop. Thank you to all of the participants for lots of great discussions, brainstorms, and forging of new collaborations. See you next year!
#genomeengineering2019
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1/ Delivery of nucleic acid therapies to cells remains a bottleneck for gene therapy. We wanted to develop a modular delivery system that would be safe and cell-type type specific, avoiding the immunogenicity of common viral vectors.
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1/x In exploring the evolution of Cas9, we identified Fanzor (Fz) as a putative RNA-guided nuclease while studying IscB, IsrB, and TnpB–collectively called OMEGA systems–in collaboration with Eugene Koonin’s group. Here, we expand our analysis of the diversity of Fz proteins,
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Happy 60th
@eric_lander
! Thank you for the family you have created for us and for continuing to be our inspiration!
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This is so exciting. So much unknown to explore!
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Congratulations
@SKonermann
and
@pdhsu
on this exciting adventure!
I am incredibly excited to announce after nearly two years in the making.
@arcinstitute
is a new, nonprofit research institute launched in collaboration with
@Stanford
,
@UCSF
, and
@UCBerkeley
that will focus on complex diseases.
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1/ We were exploring Cas9 diversity when we found IscB, a transposon-encoded protein that shares nuclease domains with Cas9. However, unlike Cas9, no RNA or CRISPR components are known to interact with it, making its function a mystery.
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There’s likely so much more physics that still await our discovery.
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2/ Using both computational and experimental approaches, we found IscB associates with a new, diverse class of large structured non-coding RNAs, termed omegaRNAs.
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Couldn’t be more proud of
@jgooten
and
@omarabudayyeh
. Good luck with your new adventure!
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9/x This work was led by postdocs Makoto Saito and Peiyu Xu in collaboration with
@GuilhemFaure
, S. Maguire,
@soumya_kannan12
,
@altaetran
, S. Vo & A. Desimone. Congratulations on a beautiful and comprehensive study!
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Congratulations
@JuliaJoung
on completing this heroic project and leading an amazing team!
Thrilled to share my primary PhD work: a Transcription Factor Atlas for understanding gene regulation and cell engineering
@CellCellPress
. We created a comprehensive TF ORF library and applied it to profile resulting expression changes. A thread 1/X
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8/x Fz shares structural similarities with TnpB and Cas12, but the interaction between the ωRNA and the catalytic domains of Fz is notably more extensive, suggesting that the ωRNA might play a role in the catalytic reactions involving Fz.
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6/ To our surprise, we also functional IscB genes in the eukaryotic cells, in the chloroplast of green algae I. tetrasporus.
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4/ Using phylogenetic analysis and enabled by collaborator (
@GCACTAATTGAGAAC
, MDlakic,
@Ivan_Bilinski
) samples from Yellowstone Lake, we identified a new Cas9 subtype II-D and show that CRISPR-Cas9 likely evolved from ancestral OMEGA systems.
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5/ Using
#AlphaFold
to model Pvc13, we predicted which part of Pvc13 contacts target cells and used this information as a guide to insert binding domains specific to human cells into Pvc13. We confirmed these PVC variants bound to and delivered cargo to the intended target cells.
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7/ Beyond IscB, we uncovered additional classes of OMEGA systems, TnpB and IsrB, that also function as programmable RNA-guided endonucleases and nickases, respectively.
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Last but not least, huge thanks to our supporters, in particular
@HHMI
,
@McGovernMIT
,
@broadinstitute
,
@NIH
,
@open_phil
, Mathers Fdn, J.&P. Poitras, M.&L.&E.Schwartz, and
@NEBiolabs
,
@Quintara_Bio
,
@Synthego
, & MileniaBiotec for their big help. 5/X
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Congratulations
@Society4Science
2019
#intelisef
finalists! You are our inspiration and our future!
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7/ This work was led by graduate student Joe Kreitz (
@kreitz_joseph
) with collaboration from MFriedrich (
@mircoscopy
), AGuru (
@Akash_Guru_
), BLash (
@blake_lash
), and MSaito.
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Congratulations
@VivianGradinaru
and
@TheHongLab
! Excited to see your creativity and impact getting recognized. Viv, we should revisit those old ideas again!
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6/ We took a similar structure-guided approach to target neurons in the mouse brain, showing in vivo delivery of a cargo protein specifically to neurons. We are continuing to expand the targeting and packaging abilities of PVCs and test them in vivo.
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We are indebted to have
@JKeithJoung
kick off GE7.0 with an exciting keynote on latest advances in genome editing.
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7/ SEND can be used to deliver different payloads including Cas9 and guide RNAs to human cells.
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2/ Given cool findings by Vivian Budnik/Travis Thomson and
@jasonsynaptic
showing the retrotransposon-derived protein ARC forms capsids and transfers mRNA between cells, we collaborated with Koonin lab to identify other retroelement-derived proteins that might form capsids.
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3/ Naturally occurring omegaRNAs contain a guide sequence that directs IscB to its target DNA. This guide can be reprogrammed to target IscB to DNA sequences.
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7/x Finally, to gain insight into the mechanism of Fz and guide future development, we used cryo-EM to resolve the structure of SpuFz1 in complex with ωRNA and target DNA at 2.7 Å.
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Endymion Wilkinson who taught me Chinese history in college just released the 6th edition of the “Chinese History” manual. It is inspiring to see how a diplomat’s passion project turned into a cornerstone resource for Sinology research.
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2/ We focused on the Photorhabdus virulence cassette (PVC), a type of CIS that is secreted by Photorhabdus and known to infect insect and mouse cells. We reconstituted PVCs in E. coli and confirmed they could attach to insect cells, their native target.
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2/x Fz1 and Fz2 share similar domain architecture and catalytic residues with the OMEGA effector TnpB and the CRISPR effector Cas12, and our analysis suggests TnpB evolved into both prokaryotic Cas12 and eukaryotic Fz.
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3/ We then explored if we could replace the endogenous cargo protein with a protein of interest. To do this, we introduced a packaging signal on a cargo protein (GFP, Cre, or ZFN), confirmed it was loaded by the PVC, and showed it functioned in recipient insect cells.
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3/x Based on this, we predicted Fz is also an RNA-guided DNA endonuclease. To test this, we first performed RNA pull-downs with Fz1 and Fz2 and found these proteins bind to the non-coding RNA found in Fz loci, confirming this region encodes an ωRNA.
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3/ A number of retroelement-derived proteins form virus-like particles and are secreted when expressed in HEK cells, including PEG10.
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4/ We focused on PEG10 because it self-assembled into capsids, was efficiently secreted as extracellular vesicles, bound its own RNA in the UTRs, and carried its own mRNA out of the cell.
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4/ To redirect the tropism of PVCs to human cells, we took advantage of the structural similarities between the PVC and contractile phage tails, modification of which can change phage targeting. Based on this, we focused our engineering efforts on Pvc13, the tail fiber protein.
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5/x We then showed that Fz1 and Fz2 can be reprogrammed to target the human genome in cells.
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It is really cool that CAST systems have evolved two unique homing mechanisms, one through hidden crRNAs and another through dedicated homing proteins. We are excited to continue contributing to the growing knowledge of CAST biology and CAST-based bioengineering tools! 5/5
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4/x We next experimentally confirmed that Fz1 and Fz2 perform ωRNA-guided DNA cleavage in a TAM-dependent manner, and obtained four active Fz orthologs (from fungus, algae, amoeba and hard clam).
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5/ Grafting the 5’ and 3’ UTRs of PEG10 onto Cre mRNA (creating a cargoRNA) along with co-expression of the fusogenic protein VSVg led to functional transfer of the Cre mRNA into loxP-GFP reporter cells.
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39
David Paez-Espino from JGI on the exploration of CRISPR diversity using the JGI database.
#genomeengineering2019
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Congratulations
@randall_platt
! Really creative!
In
@ScienceMagazine
we describe how a CRISPR-based bacterial recording system (Record-seq) captures signatures of diet, disease, and microbial interactions within the intestine – helping us understand how diet, disease, and the microbiota shape health. 1/12
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6/x To boost in vivo editing, we focused on Fz1 from the fungus Spizellomyces punctatus (SpuFz1), and optimized both the ωRNA and protein component, achieving a nearly 10-fold increase in activity (max. 18.4% indel formation) on the human genome.
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6/ We could also pseudotype these particles with a mouse endogenous fusogenic membrane protein, SynA, to deliver mRNA to fibroblasts.
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