Toward precision CRISPR DNA fragment editing and predictable 3D genome engineering.

Abstract:

:Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of three-dimensional (3D) genomes. CRISPR gene editing results from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break (DSB) repair machineries. Recent studies revealed, however, that the CRISPR genome editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise one-dimensional (1D) gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.

journal_name

J Mol Cell Biol

authors

Wu Q,Shou J

doi

10.1093/jmcb/mjaa060

subject

Has Abstract

pub_date

2020-10-30 00:00:00

eissn

1674-2788

issn

1759-4685

pii

5943882

pub_type

杂志文章
  • Vertebrate Dynein-f depends on Wdr78 for axonemal localization and is essential for ciliary beat.

    abstract::Motile cilia and flagella are microtubule-based organelles important for cell locomotion and extracellular liquid flow through beating. Although axonenal dyneins that drive ciliary beat have been extensively studied in unicellular Chlamydomonas, to what extent such knowledge can be applied to vertebrate is poorly know...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjy043

    authors: Zhang Y,Chen Y,Zheng J,Wang J,Duan S,Zhang W,Yan X,Zhu X

    更新日期:2019-05-01 00:00:00

  • Myeloid adrenergic signaling via CaMKII forms a feedforward loop of catecholamine biosynthesis.

    abstract::Type 2 immune response has been shown to facilitate cold-induced thermogenesis and browning of white fat. However, whether alternatively activated macrophages produce catecholamine and substantially promote adaptive thermogenesis in adipose tissue remains controversial. Here, we show that tyrosine hydroxylase (TyrH), ...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjx046

    authors: Luo Y,Liu B,Yang X,Ma X,Zhang X,Bragin DE,Yang XO,Huang W,Liu M

    更新日期:2017-10-01 00:00:00

  • Molecular suicide notes: last call from apoptosing cells.

    abstract::Dying cells actively attract professional phagocytes by sending out soluble 'find-me' signals. The characterization and identification of the corresponding molecular entities have revealed that 'find-me' signals come in different flavors, including peptides, proteins, lipids and complex structures, such as apoptotic m...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjp045

    authors: Peter C,Wesselborg S,Lauber K

    更新日期:2010-04-01 00:00:00

  • Extracellular vesicle-mediated transfer of donor genomic DNA to recipient cells is a novel mechanism for genetic influence between cells.

    abstract::Extracellular vesicles (EVs) carry signals within or at their limiting membranes, providing a mechanism by which cells can exchange more complex information than what was previously thought. In addition to mRNAs and microRNAs, there are DNA fragments in EVs. Solexa sequencing indicated the presence of at least 16434 g...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjt011

    authors: Cai J,Han Y,Ren H,Chen C,He D,Zhou L,Eisner GM,Asico LD,Jose PA,Zeng C

    更新日期:2013-08-01 00:00:00

  • The role of RAD9 in tumorigenesis.

    abstract::RAD9 regulates multiple cellular processes that influence genomic integrity, and for at least some of its functions the protein acts as part of a heterotrimeric complex bound to HUS1 and RAD1 proteins. RAD9 participates in DNA repair, including base excision repair, homologous recombination repair and mismatch repair,...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章,评审

    doi:10.1093/jmcb/mjq039

    authors: Lieberman HB,Bernstock JD,Broustas CG,Hopkins KM,Leloup C,Zhu A

    更新日期:2011-02-01 00:00:00

  • Oxygen sufficiency controls TOP mRNA translation via the TSC-Rheb-mTOR pathway in a 4E-BP-independent manner.

    abstract::Cells encountering hypoxic stress conserve resources and energy by downregulating the protein synthesis. Here we demonstrate that one mechanism in this response is the translational repression of TOP mRNAs that encode components of the translational apparatus. This mode of regulation involves TSC and Rheb, as knockout...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mju008

    authors: Miloslavski R,Cohen E,Avraham A,Iluz Y,Hayouka Z,Kasir J,Mudhasani R,Jones SN,Cybulski N,Rüegg MA,Larsson O,Gandin V,Rajakumar A,Topisirovic I,Meyuhas O

    更新日期:2014-06-01 00:00:00

  • miR-221/222 activate the Wnt/β-catenin signaling to promote triple-negative breast cancer.

    abstract::Triple-negative breast cancer (TNBC), characterized by the lack of expression of the estrogen receptor, the progesterone receptor, and the human epidermal growth factor receptor 2, is an aggressive form of cancer that conveys unpredictable and poor prognosis due to limited treatment options and lack of effective targe...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjy041

    authors: Liu S,Wang Z,Liu Z,Shi S,Zhang Z,Zhang J,Lin H

    更新日期:2018-08-01 00:00:00

  • Generation of liver bipotential organoids with a small-molecule cocktail.

    abstract::Understanding the mechanism of how cholangiocytes (liver ductal cells) are activated upon liver injury and specified to hepatocytes would permit liver regenerative medicine. Here we achieved long-term in vitro expansion of mouse liver organoids by modulating signaling pathways with a combination of three small-molecul...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjaa010

    authors: Wang X,Ni C,Jiang N,Wei J,Liang J,Zhao B,Lin X

    更新日期:2020-08-01 00:00:00

  • Adaptor protein APPL1 links neuronal activity to chromatin remodeling in cultured hippocampal neurons.

    abstract::Local signaling events at synapses or axon terminals are communicated to the nucleus to elicit transcriptional responses, and thereby translate information about the external environment into internal neuronal representations. This retrograde signaling is critical to dendritic growth, synapse development, and neuronal...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjaa058

    authors: Wu Y,Lv X,Wang H,Qian K,Ding J,Wang J,Hua S,Sun T,Zhou Y,Yu L,Qiu S

    更新日期:2020-10-26 00:00:00

  • Haploinsufficiency of the TDP43 ubiquitin E3 ligase RNF220 leads to ALS-like motor neuron defects in the mouse.

    abstract::TDP43 pathology is seen in a large majority of amyotrophic lateral sclerosis (ALS) cases, suggesting a central pathogenic role of this regulatory protein. Clarifying the molecular mechanism controlling TDP43 stability and subcellular location might provide important insights into ALS therapy. The ubiquitin E3 ligase R...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjaa072

    authors: Ma P,Li Y,Wang H,Mao B

    更新日期:2021-01-02 00:00:00

  • Cancer and neurodegenerative disorders: pathogenic convergence through microRNA regulation.

    abstract::Although cancer and neurodegenerative disease are two distinct pathological disorders, emerging evidence indicates that these two types of disease share common mechanisms of genetic and molecular abnormalities. Recent studies show that individual microRNAs (miRNAs) could be involved in the pathology of both diseases, ...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章,评审

    doi:10.1093/jmcb/mjq058

    authors: Du L,Pertsemlidis A

    更新日期:2011-06-01 00:00:00

  • Embryonic hematopoiesis in vertebrate somites gives rise to definitive hematopoietic stem cells.

    abstract::Hematopoietic stem cells (HSCs) replenish all types of blood cells. It is debating whether HSCs in adults solely originate from the aorta-gonad-mesonephros (AGM) region, more specifically, the dorsal aorta, during embryogenesis. Here, we report that somite hematopoiesis, a previously unwitnessed hematopoiesis, can gen...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjw024

    authors: Qiu J,Fan X,Wang Y,Jin H,Song Y,Han Y,Huang S,Meng Y,Tang F,Meng A

    更新日期:2016-08-01 00:00:00

  • The long and the short of it: the MDM4 tail so far.

    abstract::The mouse double minute 4 (MDM4) is emerging from the shadow of its more famous relative MDM2 and is starting to steal the limelight, largely due to its therapeutic possibilities. MDM4 is a vital regulator of the tumor suppressor p53. It restricts p53 transcriptional activity and also, at least in development, facilit...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章,评审

    doi:10.1093/jmcb/mjz007

    authors: Haupt S,Mejía-Hernández JO,Vijayakumaran R,Keam SP,Haupt Y

    更新日期:2019-03-01 00:00:00

  • Ablation of Zfhx4 results in early postnatal lethality by disrupting the respiratory center in mice.

    abstract::Breathing is an integrated motor behavior that is driven and controlled by a network of brainstem neurons. Zfhx4 is a zinc finger transcription factor and our results showed that it was specifically expressed in several regions of the mouse brainstem. Mice lacking Zfhx4 died shortly after birth from an apparent inabil...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjaa081

    authors: Zhang M,Du S,Ou H,Cui R,Jiang N,Lin Y,Ge R,Ma D,Zhang J

    更新日期:2021-01-20 00:00:00

  • The GYF domain protein CD2BP2 is critical for embryogenesis and podocyte function.

    abstract::Scaffolding proteins play pivotal roles in the assembly of macromolecular machines such as the spliceosome. The adaptor protein CD2BP2, originally identified as a binding partner of the adhesion molecule CD2, is a pre-spliceosomal assembly factor that utilizes its glycine-tyrosine-phenylalanine (GYF) domain to co-loca...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjv039

    authors: Albert GI,Schell C,Kirschner KM,Schäfer S,Naumann R,Müller A,Kretz O,Kuropka B,Girbig M,Hübner N,Krause E,Scholz H,Huber TB,Knobeloch KP,Freund C

    更新日期:2015-10-01 00:00:00

  • SP1 governs primordial folliculogenesis by regulating pregranulosa cell development in mice.

    abstract::Establishment of the primordial follicle (PF) pool is pivotal for the female reproductive lifespan; however, the mechanism of primordial folliculogenesis is poorly understood. Here, the transcription factor SP1 was shown to be essential for PF formation in mice. Our results showed that SP1 is present in both oocytes a...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjz059

    authors: Cai H,Liu B,Wang H,Sun G,Feng L,Chen Z,Zhou J,Zhang J,Zhang T,He M,Yang T,Guo Q,Teng Z,Xin Q,Zhou B,Zhang H,Xia G,Wang C

    更新日期:2020-04-24 00:00:00

  • Proteome-wide Data Analysis Reveals Tissue-specific Network Associated with SARS-CoV-2 Infection.

    abstract::For patients with COVID-19 caused by SARS-CoV-2, the damages to multiple organs have been clinically observed. Since most of current investigations for virus-host interaction are based on cell level, there is an urgent demand to probe tissue-specific features associated with SARS-CoV-2 infection. Based on collected pr...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjaa033

    authors: Feng L,Yin YY,Liu CH,Xu KR,Li QR,Wu JR,Zeng R

    更新日期:2020-07-08 00:00:00

  • BMP signaling promotes the growth of primary human colon carcinomas in vivo.

    abstract::Human colon carcinomas (CCs) represent a growing worldwide problem. One of the pathways that has been negatively implicated in the genesis of CCs is triggered by bone morphogenetic protein (BMP) ligands, which activate BMP receptors leading to the function of SMAD proteins in the nucleus. BMP signaling is altered in f...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjq035

    authors: Lorente-Trigos A,Varnat F,Melotti A,Ruiz i Altaba A

    更新日期:2010-12-01 00:00:00

  • A role for paralog-specific sumoylation in histone deacetylase 1 stability.

    abstract::Histone deacetylase 1 (HDAC1) is an essential epigenetic regulator belonging to a highly conserved family of deacetylases. Increased HDAC1 activity and expression often correlates with neoplastic transformation. Here we show how specific modification of HDAC1 by SUMO1, but not by SUMO2, facilitates HDAC1 degradation. ...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjt032

    authors: Citro S,Jaffray E,Hay RT,Seiser C,Chiocca S

    更新日期:2013-12-01 00:00:00

  • An HBV-encoded miRNA activates innate immunity to restrict HBV replication.

    abstract::We previously identified that hepatitis B virus (HBV) encodes a microRNA (HBV-miR-3) that restrains HBV replication by targeting the HBV transcript. However, whether HBV-miR-3 affects host innate immunity to modulate HBV replication remains unclear. Here, we examined the vital functions of HBV-miR-3 in the innate immu...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjz104

    authors: Zhao X,Sun L,Mu T,Yi J,Ma C,Xie H,Liu M,Tang H

    更新日期:2020-05-18 00:00:00

  • Cigarette smoke-induced cell cycle arrest in spermatocytes [GC-2spd(ts)] is mediated through crosstalk between Ahr-Nrf2 pathway and MAPK signaling.

    abstract::Our earlier studies have demonstrated that the cigarette smoke in the form of cigarette smoke condensate (CSC) causes growth arrest of a mouse spermatocyte cell line [GC-2spd(ts)] through activation of the AHR-NRF2 pathway. The present study demonstrates the CSC-activated p38 and ERK MAPK signaling in GC-2spd(ts) via ...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mju049

    authors: Esakky P,Hansen DA,Drury AM,Moley KH

    更新日期:2015-02-01 00:00:00

  • Smad1/5/8 are myogenic regulators of murine and human mesoangioblasts.

    abstract::Mesoangioblasts (MABs) are vessel-associated stem cells that express pericyte marker genes and participate in skeletal muscle regeneration. Molecular circuits that regulate the myogenic commitment of MABs are still poorly characterized. The critical role of bone morphogenetic protein (BMP) signalling during proliferat...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjv059

    authors: Costamagna D,Quattrocelli M,van Tienen F,Umans L,de Coo IF,Zwijsen A,Huylebroeck D,Sampaolesi M

    更新日期:2016-02-01 00:00:00

  • Egg CD9 protein tides correlated with sperm oscillations tune the gamete fusion ability in mammal.

    abstract::Mammalian fertilization involves membrane events-adhesion, fusion, sperm engulfment, membrane block to polyspermy-whose causes remain largely unknown. Recently, specific oscillations of the sperm in contact with the egg were shown to be necessary for fusion. Using a microfluidic chip to impose the venue for the encoun...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjy005

    authors: Ravaux B,Favier S,Perez E,Gourier C

    更新日期:2018-12-01 00:00:00

  • NKT cell self-reactivity: evolutionary master key of immune homeostasis?

    abstract::Complex immune responses have evolved to protect multicellular organisms against the invasion of pathogens. This has exerted strong developmental pressure for specialized functions that can also limit damage to self-tissue. Two arms of immunity, the innate and adaptive immune systems, have evolved for quick, non-speci...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章,评审

    doi:10.1093/jmcb/mjr035

    authors: Issazadeh-Navikas S

    更新日期:2012-04-01 00:00:00

  • Role of the lncRNA-p53 regulatory network in cancer.

    abstract::Advances in functional genomics have led to discovery of a large group of previous uncharacterized long non-coding RNAs (lncRNAs). Emerging evidence indicates that lncRNAs may serve as master gene regulators through various mechanisms. Dysregulation of lncRNAs is often associated with a variety of human diseases inclu...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章,评审

    doi:10.1093/jmcb/mju013

    authors: Zhang A,Xu M,Mo YY

    更新日期:2014-06-01 00:00:00

  • AFF3-DNA methylation interplay in maintaining the mono-allelic expression pattern of XIST in terminally differentiated cells.

    abstract::X chromosome inactivation and genomic imprinting are two classic epigenetic regulatory processes that cause mono-allelic gene expression. In female mammals, mono-allelic expression of the long non-coding RNA gene X-inactive specific transcript (XIST) is essential for initiation of X chromosome inactivation upon differ...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjy074

    authors: Zhang Y,Wang C,Liu X,Yang Q,Ji H,Yang M,Xu M,Zhou Y,Xie W,Luo Z,Lin C

    更新日期:2019-09-19 00:00:00

  • Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks.

    abstract::Although genome-wide association studies (GWAS) have successfully identified thousands of genomic loci associated with hundreds of complex traits in the past decade, the debate about such problems as missing heritability and weak interpretability has been appealing for effective computational methods to facilitate the...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjx059

    authors: Wu M,Lin Z,Ma S,Chen T,Jiang R,Wong WH

    更新日期:2017-12-01 00:00:00

  • The crossregulation between ERK and PI3K signaling pathways determines the tumoricidal efficacy of MEK inhibitor.

    abstract::MEK inhibitor has been highlighted as a promising anti-tumor drug but its effect has been reported as varying over a wide range depending on patho-physiological conditions. In this study, we employed a systems approach by combining biochemical experimentation with in silico simulations to investigate the resistance me...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjs021

    authors: Won JK,Yang HW,Shin SY,Lee JH,Heo WD,Cho KH

    更新日期:2012-06-01 00:00:00

  • Mdm2 as a chromatin modifier.

    abstract::Mdm2 is the key negative regulator of the tumour suppressor p53, making it an attractive target for anti-cancer drug design. We recently identified a new role of Mdm2 in gene repression through its direct interaction with several proteins of the polycomb group (PcG) family. PcG proteins form polycomb repressive comple...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章,评审

    doi:10.1093/jmcb/mjw046

    authors: Wienken M,Moll UM,Dobbelstein M

    更新日期:2017-02-01 00:00:00

  • NSD3S stabilizes MYC through hindering its interaction with FBXW7.

    abstract::The MYC transcription factor plays a key role in cell growth control. Enhanced MYC protein stability has been found to promote tumorigenesis. Thus, understanding how MYC stability is controlled may have significant implications for revealing MYC-driven growth regulatory mechanisms in physiological and pathological pro...

    journal_title:Journal of molecular cell biology

    pub_type: 杂志文章

    doi:10.1093/jmcb/mjz098

    authors: Gonzalez-Pecchi V,Kwan AK,Doyle S,Ivanov AA,Du Y,Fu H

    更新日期:2020-07-03 00:00:00