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Article ; Online: JIP2 haploinsufficiency contributes to neurodevelopmental abnormalities in human pluripotent stem cell-derived neural progenitors and cortical neurons.

Roessler, Reinhard / Goldmann, Johanna / Shivalila, Chikdu / Jaenisch, Rudolf

Life science alliance

2018 Volume 1, Issue 4, Page(s) e201800094

Abstract: Phelan-McDermid syndrome (also known as 22q13.3 deletion syndrome) is a syndromic form of autism spectrum disorder and currently thought to be caused by heterozygous loss ... ...

Abstract	Phelan-McDermid syndrome (also known as 22q13.3 deletion syndrome) is a syndromic form of autism spectrum disorder and currently thought to be caused by heterozygous loss of
Language	English
Publishing date	2018-06-25
Publishing country	United States
Document type	Journal Article
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.201800094
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Article ; Online: Parent-of-Origin DNA Methylation Dynamics during Mouse Development.

Stelzer, Yonatan / Wu, Hao / Song, Yuelin / Shivalila, Chikdu S / Markoulaki, Styliani / Jaenisch, Rudolf

Cell reports

2016 Volume 16, Issue 12, Page(s) 3167–3180

Abstract: Parent-specific differentially methylated regions (DMRs) are established during gametogenesis and regulate parent-specific expression of imprinted genes. Monoallelic expression of imprinted genes is essential for development, suggesting that imprints are ...

Abstract	Parent-specific differentially methylated regions (DMRs) are established during gametogenesis and regulate parent-specific expression of imprinted genes. Monoallelic expression of imprinted genes is essential for development, suggesting that imprints are faithfully maintained in embryos and adults. To test this hypothesis, we targeted a reporter for genomic methylation to the imprinted Dlk1-Dio3 intergenic DMR (IG-DMR) to assess the methylation of both parental alleles at single-cell resolution. Biallelic gain or loss of IG-DMR methylation occurred in a small fraction of mouse embryonic stem cells, significantly affecting developmental potency. Mice carrying the reporter in either parental allele showed striking parent-specific changes in IG-DMR methylation, causing substantial and consistent tissue- and cell-type-dependent signatures in embryos and postnatal animals. Furthermore, dynamics in DNA methylation persisted during adult neurogenesis, resulting in inter-individual diversity. This substantial cell-cell DNA methylation heterogeneity implies that dynamic DNA methylation variations in the adult may be of functional importance.
MeSH term(s)	Animals ; DNA Methylation/genetics ; Embryonic Development/genetics ; Genomic Imprinting/genetics ; Mice ; Neurogenesis/genetics
Language	English
Publishing date	2016-06-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2016.08.066
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Article ; Online: Stereochemistry Enhances Potency, Efficacy, and Durability of

Byrne, Michael / Vathipadiekal, Vinod / Apponi, Luciano / Iwamoto, Naoki / Kandasamy, Pachamuthu / Longo, Kenneth / Liu, Fangjun / Looby, Richard / Norwood, Lauren / Shah, Anee / Shelke, Juili Dilip / Shivalila, Chikdu / Yang, Hailin / Yin, Yuan / Guo, Lankai / Bowman, Keith / Vargeese, Chandra

Translational vision science & technology

2021 Volume 10, Issue 1, Page(s) 23

Abstract: Purpose: Antisense oligonucleotides have been under investigation as potential therapeutics for many diseases, including inherited retinal diseases. Chemical modifications, such as chiral phosphorothioate (PS) backbone modification, are often used to ... ...

Abstract	Purpose: Antisense oligonucleotides have been under investigation as potential therapeutics for many diseases, including inherited retinal diseases. Chemical modifications, such as chiral phosphorothioate (PS) backbone modification, are often used to improve stability and pharmacokinetic properties of these molecules. We aimed to generate a stereopure Methods: We generated a stereopure oligonucleotide (MALAT1-200) and assessed the potency, efficacy, and durability of its Results: The activity of the stereopure oligonucleotide is superior to its stereorandom mixture counterpart with the same sequence and chemical modification pattern in in vitro assays, in vivo mouse and NHP eyes, and ex vivo human retina cultures. Findings in NHPs showed durable activity of the stereopure oligonucleotide in the retina, with nearly 95% reduction of Conclusions: An optimized, stereopure antisense oligonucleotide shows enhanced potency, efficacy, and durability of Translational relevance: As novel therapeutics, stereopure oligonucleotides have the potential to enable infrequent administration and low-dose regimens for patients with genetic diseases of the eye.
MeSH term(s)	Adenocarcinoma of Lung ; Animals ; Eye ; Humans ; Lung Neoplasms ; Mice ; Oligonucleotides ; Oligonucleotides, Antisense/genetics
Chemical Substances	Oligonucleotides ; Oligonucleotides, Antisense
Language	English
Publishing date	2021-01-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2674602-5
ISSN	2164-2591 ; 2164-2591
ISSN (online)	2164-2591
ISSN	2164-2591
DOI	10.1167/tvst.10.1.23
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Article ; Online: Tracing dynamic changes of DNA methylation at single-cell resolution.

Stelzer, Yonatan / Shivalila, Chikdu Shakti / Soldner, Frank / Markoulaki, Styliani / Jaenisch, Rudolf

Cell

2015 Volume 163, Issue 1, Page(s) 218–229

Abstract: Mammalian DNA methylation plays an essential role in development. To date, only snapshots of different mouse and human cell types have been generated, providing a static view on DNA methylation. To enable monitoring of methylation status as it changes ... ...

Abstract	Mammalian DNA methylation plays an essential role in development. To date, only snapshots of different mouse and human cell types have been generated, providing a static view on DNA methylation. To enable monitoring of methylation status as it changes over time, we establish a reporter of genomic methylation (RGM) that relies on a minimal imprinted gene promoter driving a fluorescent protein. We show that insertion of RGM proximal to promoter-associated CpG islands reports the gain or loss of DNA methylation. We further utilized RGM to report endogenous methylation dynamics of non-coding regulatory elements, such as the pluripotency-specific super enhancers of Sox2 and miR290. Loci-specific DNA methylation changes and their correlation with transcription were visualized during cell-state transition following differentiation of mouse embryonic stem cells and during reprogramming of somatic cells to pluripotency. RGM will allow the investigation of dynamic methylation changes during development and disease at single-cell resolution.
MeSH term(s)	Animals ; CpG Islands ; DNA Methylation ; DNA Modification Methylases/metabolism ; Embryonic Stem Cells ; Enhancer Elements, Genetic ; Humans ; Mice ; MicroRNAs/metabolism ; Promoter Regions, Genetic ; SOXB1 Transcription Factors/metabolism ; Single-Cell Analysis
Chemical Substances	MIRN290 microRNA, mouse ; MicroRNAs ; SOXB1 Transcription Factors ; Sox2 protein, mouse ; DNA Modification Methylases (EC 2.1.1.-)
Language	English
Publishing date	2015-09-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2015.08.046
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Article ; Online: Two independent regions of simian virus 40 T antigen increase CBP/p300 levels, alter patterns of cellular histone acetylation, and immortalize primary cells.

Sáenz Robles, Maria Teresa / Shivalila, Chikdu / Wano, Jeremy / Sorrells, Shelly / Roos, Alison / Pipas, James M

Journal of virology

2013 Volume 87, Issue 24, Page(s) 13499–13509

Abstract: Simian virus 40 (SV40) large T antigen (SVT) interferes with normal cell regulation and thus has been used to identify cellular components controlling proliferation and homeostasis. We have previously shown that SVT-mediated transformation requires ... ...

Abstract	Simian virus 40 (SV40) large T antigen (SVT) interferes with normal cell regulation and thus has been used to identify cellular components controlling proliferation and homeostasis. We have previously shown that SVT-mediated transformation requires interaction with the histone acetyltransferases (HATs) CBP/p300 and now report that the ectopic expression of SVT in several cell types in vivo and in vitro results in a significant increase in the steady-state levels of CBP/p300. Furthermore, SVT-expressing cells contain higher levels of acetylated CBP/p300, a modification that has been linked to increased HAT activity. Concomitantly, the acetylation levels of histone residues H3K56 and H4K12 are markedly increased in SVT-expressing cells. Other polyomavirus-encoded large T antigens also increase the levels of CBP/p300 and sustain a rise in the acetylation levels of H3K56 and H4K12. SVT does not affect the transcription of CBP/p300, but rather, alters their overall levels through increasing the loading of CBP/p300 mRNAs onto polysomes. Two distinct regions within SVT, one located in the amino terminus and one in the carboxy terminus, can independently alter both the levels of CBP/p300 and the loading of CBP/p300 transcripts onto polysomes. Within the amino-terminal fragment, a functional J domain is necessary for increasing CBP/p300 and specific histone acetylation levels, as well as for immortalizing primary cells. These studies uncover the action of polyomavirus T antigens on cellular CBP/p300 and suggest that additional mechanisms are used by T antigens to induce cell immortalization and transformation.
MeSH term(s)	Acetylation ; Amino Acid Motifs ; Animals ; Antigens, Polyomavirus Transforming/chemistry ; Antigens, Polyomavirus Transforming/genetics ; Antigens, Polyomavirus Transforming/metabolism ; CREB-Binding Protein/genetics ; CREB-Binding Protein/metabolism ; Cell Transformation, Viral ; Cells, Cultured ; E1A-Associated p300 Protein/genetics ; E1A-Associated p300 Protein/metabolism ; Fibroblasts/metabolism ; Fibroblasts/virology ; Histones/chemistry ; Histones/genetics ; Histones/metabolism ; Humans ; Polyomavirus Infections/enzymology ; Polyomavirus Infections/genetics ; Polyomavirus Infections/metabolism ; Polyomavirus Infections/virology ; Simian virus 40/chemistry ; Simian virus 40/genetics ; Simian virus 40/physiology ; Tumor Virus Infections/enzymology ; Tumor Virus Infections/genetics ; Tumor Virus Infections/metabolism ; Tumor Virus Infections/virology
Chemical Substances	Antigens, Polyomavirus Transforming ; Histones ; CREB-Binding Protein (EC 2.3.1.48) ; Crebbp protein, mouse (EC 2.3.1.48) ; E1A-Associated p300 Protein (EC 2.3.1.48) ; Ep300 protein, mouse (EC 2.3.1.48)
Language	English
Publishing date	2013-10-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.02658-13
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Article ; Online: One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering.

Yang, Hui / Wang, Haoyi / Shivalila, Chikdu S / Cheng, Albert W / Shi, Linyu / Jaenisch, Rudolf

Cell

2013 Volume 154, Issue 6, Page(s) 1370–1379

Abstract: The type II bacterial CRISPR/Cas system is a novel genome-engineering technology with the ease of multiplexed gene targeting. Here, we created reporter and conditional mutant mice by coinjection of zygotes with Cas9 mRNA and different guide RNAs (sgRNAs) ...

Abstract	The type II bacterial CRISPR/Cas system is a novel genome-engineering technology with the ease of multiplexed gene targeting. Here, we created reporter and conditional mutant mice by coinjection of zygotes with Cas9 mRNA and different guide RNAs (sgRNAs) as well as DNA vectors of different sizes. Using this one-step procedure we generated mice carrying a tag or a fluorescent reporter construct in the Nanog, the Sox2, and the Oct4 gene as well as Mecp2 conditional mutant mice. In addition, using sgRNAs targeting two separate sites in the Mecp2 gene, we produced mice harboring the predicted deletions of about 700 bps. Finally, we analyzed potential off-targets of five sgRNAs in gene-modified mice and ESC lines and identified off-target mutations in only rare instances.
MeSH term(s)	Animals ; Base Sequence ; Gene Targeting/methods ; Genetic Engineering ; Mice/genetics ; Mutation
Language	English
Publishing date	2013-08-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2013.08.022
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Article ; Online: Endogenous ADAR-mediated RNA editing in non-human primates using stereopure chemically modified oligonucleotides.

Monian, Prashant / Shivalila, Chikdu / Lu, Genliang / Shimizu, Mamoru / Boulay, David / Bussow, Karley / Byrne, Michael / Bezigian, Adam / Chatterjee, Arindom / Chew, David / Desai, Jigar / Favaloro, Frank / Godfrey, Jack / Hoss, Andrew / Iwamoto, Naoki / Kawamoto, Tomomi / Kumarasamy, Jayakanthan / Lamattina, Anthony / Lindsey, Amber /

Liu, Fangjun / Looby, Richard / Marappan, Subramanian / Metterville, Jake / Murphy, Ronelle / Rossi, Jeff / Pu, Tom / Bhattarai, Bijay / Standley, Stephany / Tripathi, Snehlata / Yang, Hailin / Yin, Yuan / Yu, Hui / Zhou, Cong / Apponi, Luciano H / Kandasamy, Pachamuthu / Vargeese, Chandra

Nature biotechnology

2022 Volume 40, Issue 7, Page(s) 1093–1102

Abstract: Technologies that recruit and direct the activity of endogenous RNA-editing enzymes to specific cellular RNAs have therapeutic potential, but translating them from cell culture into animal models has been challenging. Here we describe short, chemically ... ...

Abstract	Technologies that recruit and direct the activity of endogenous RNA-editing enzymes to specific cellular RNAs have therapeutic potential, but translating them from cell culture into animal models has been challenging. Here we describe short, chemically modified oligonucleotides called AIMers that direct efficient and specific A-to-I editing of endogenous transcripts by endogenous adenosine deaminases acting on RNA (ADAR) enzymes, including the ubiquitously and constitutively expressed ADAR1 p110 isoform. We show that fully chemically modified AIMers with chimeric backbones containing stereopure phosphorothioate and nitrogen-containing linkages based on phosphoryl guanidine enhanced potency and editing efficiency 100-fold compared with those with uniformly phosphorothioate-modified backbones in vitro. In vivo, AIMers targeted to hepatocytes with N-acetylgalactosamine achieve up to 50% editing with no bystander editing of the endogenous ACTB transcript in non-human primate liver, with editing persisting for at least one month. These results support further investigation of the therapeutic potential of stereopure AIMers.
MeSH term(s)	Animals ; Oligonucleotides ; Primates/genetics ; Primates/metabolism ; RNA ; RNA Editing/genetics ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
Chemical Substances	Oligonucleotides ; RNA-Binding Proteins ; RNA (63231-63-0)
Language	English
Publishing date	2022-03-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-022-01225-1
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Article ; Online: One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering.

Wang, Haoyi / Yang, Hui / Shivalila, Chikdu S / Dawlaty, Meelad M / Cheng, Albert W / Zhang, Feng / Jaenisch, Rudolf

Cell

2013 Volume 153, Issue 4, Page(s) 910–918

Abstract: Mice carrying mutations in multiple genes are traditionally generated by sequential recombination in embryonic stem cells and/or time-consuming intercrossing of mice with a single mutation. The CRISPR/Cas system has been adapted as an efficient gene- ... ...

Abstract	Mice carrying mutations in multiple genes are traditionally generated by sequential recombination in embryonic stem cells and/or time-consuming intercrossing of mice with a single mutation. The CRISPR/Cas system has been adapted as an efficient gene-targeting technology with the potential for multiplexed genome editing. We demonstrate that CRISPR/Cas-mediated gene editing allows the simultaneous disruption of five genes (Tet1, 2, 3, Sry, Uty--8 alleles) in mouse embryonic stem (ES) cells with high efficiency. Coinjection of Cas9 mRNA and single-guide RNAs (sgRNAs) targeting Tet1 and Tet2 into zygotes generated mice with biallelic mutations in both genes with an efficiency of 80%. Finally, we show that coinjection of Cas9 mRNA/sgRNAs with mutant oligos generated precise point mutations simultaneously in two target genes. Thus, the CRISPR/Cas system allows the one-step generation of animals carrying mutations in multiple genes, an approach that will greatly accelerate the in vivo study of functionally redundant genes and of epistatic gene interactions.
MeSH term(s)	Animals ; Base Sequence ; Embryonic Stem Cells/metabolism ; Female ; Gene Targeting/methods ; Male ; Mice/genetics ; Mice, Inbred C57BL ; Mice, Inbred DBA ; Molecular Sequence Data ; RNA, Small Untranslated
Chemical Substances	RNA, Small Untranslated
Language	English
Publishing date	2013-05-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2013.04.025
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression.

Soldner, Frank / Stelzer, Yonatan / Shivalila, Chikdu S / Abraham, Brian J / Latourelle, Jeanne C / Barrasa, M Inmaculada / Goldmann, Johanna / Myers, Richard H / Young, Richard A / Jaenisch, Rudolf

Nature

2016 Volume 533, Issue 7601, Page(s) 95–99

Abstract: Genome-wide association studies (GWAS) have identified numerous genetic variants associated with complex diseases, but mechanistic insights are impeded by a lack of understanding of how specific risk variants functionally contribute to the underlying ... ...

Abstract	Genome-wide association studies (GWAS) have identified numerous genetic variants associated with complex diseases, but mechanistic insights are impeded by a lack of understanding of how specific risk variants functionally contribute to the underlying pathogenesis. It has been proposed that cis-acting effects of non-coding risk variants on gene expression are a major factor for phenotypic variation of complex traits and disease susceptibility. Recent genome-scale epigenetic studies have highlighted the enrichment of GWAS-identified variants in regulatory DNA elements of disease-relevant cell types. Furthermore, single nucleotide polymorphism (SNP)-specific changes in transcription factor binding are correlated with heritable alterations in chromatin state and considered a major mediator of sequence-dependent regulation of gene expression. Here we describe a novel strategy to functionally dissect the cis-acting effect of genetic risk variants in regulatory elements on gene expression by combining genome-wide epigenetic information with clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9 genome editing in human pluripotent stem cells. By generating a genetically precisely controlled experimental system, we identify a common Parkinson's disease associated risk variant in a non-coding distal enhancer element that regulates the expression of α-synuclein (SNCA), a key gene implicated in the pathogenesis of Parkinson's disease. Our data suggest that the transcriptional deregulation of SNCA is associated with sequence-dependent binding of the brain-specific transcription factors EMX2 and NKX6-1. This work establishes an experimental paradigm to functionally connect genetic variation with disease-relevant phenotypes.
MeSH term(s)	Alleles ; Brain/metabolism ; CRISPR-Cas Systems/genetics ; Enhancer Elements, Genetic/genetics ; Epigenesis, Genetic/genetics ; Gene Expression Regulation ; Genetic Engineering ; Genetic Predisposition to Disease/genetics ; Genome, Human/genetics ; Homeodomain Proteins/metabolism ; Humans ; Models, Genetic ; Parkinson Disease/genetics ; Pluripotent Stem Cells/metabolism ; Risk ; Transcription Factors/metabolism ; alpha-Synuclein/genetics
Chemical Substances	Homeodomain Proteins ; NKX6-1 protein, human ; Transcription Factors ; alpha-Synuclein ; empty spiracles homeobox proteins
Language	English
Publishing date	2016-05-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature17939
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Article ; Online: Alternative SET/TAFI Promoters Regulate Embryonic Stem Cell Differentiation.

Edupuganti, Raghu Ram / Harikumar, Arigela / Aaronson, Yair / Biran, Alva / Sailaja, Badi Sri / Nissim-Rafinia, Malka / Azad, Gajendra Kumar / Cohen, Malkiel A / Park, Jung Eun / Shivalila, Chikdu S / Markoulaki, Styliani / Sze, Siu Kwan / Jaenisch, Rudolf / Meshorer, Eran

Stem cell reports

2017 Volume 9, Issue 4, Page(s) 1291–1303

Abstract: Embryonic stem cells (ESCs) are regulated by pluripotency-related transcription factors in concert with chromatin regulators. To identify additional stem cell regulators, we screened a library of endogenously labeled fluorescent fusion proteins in mouse ... ...

Abstract	Embryonic stem cells (ESCs) are regulated by pluripotency-related transcription factors in concert with chromatin regulators. To identify additional stem cell regulators, we screened a library of endogenously labeled fluorescent fusion proteins in mouse ESCs for fluorescence loss during differentiation. We identified SET, which displayed a rapid isoform shift during early differentiation from the predominant isoform in ESCs, SETα, to the primary isoform in differentiated cells, SETβ, through alternative promoters. SETα is selectively bound and regulated by pluripotency factors. SET depletion causes proliferation slowdown and perturbed neuronal differentiation in vitro and developmental arrest in vivo, and photobleaching methods demonstrate SET's role in maintaining a dynamic chromatin state in ESCs. This work identifies an important regulator of pluripotency and early differentiation, which is controlled by alternative promoter usage.
MeSH term(s)	Animals ; Cell Differentiation/genetics ; Cell Proliferation ; Cell Survival/genetics ; Chromatin Assembly and Disassembly ; Embryonic Stem Cells/cytology ; Embryonic Stem Cells/metabolism ; Gene Expression Regulation, Developmental ; Histone Acetyltransferases/genetics ; Histones/metabolism ; Mice ; Mouse Embryonic Stem Cells/cytology ; Mouse Embryonic Stem Cells/metabolism ; Neoplasm Proteins/genetics ; Nerve Tissue Proteins/genetics ; Neural Plate/cytology ; Octamer Transcription Factor-3/metabolism ; Promoter Regions, Genetic ; Protein Isoforms ; TATA-Binding Protein Associated Factors/genetics ; Transcription Factor TFIID/genetics
Chemical Substances	Histones ; Neoplasm Proteins ; Nerve Tissue Proteins ; Octamer Transcription Factor-3 ; Protein Isoforms ; Sh3kbp1 protein, mouse ; TATA-Binding Protein Associated Factors ; Transcription Factor TFIID ; Histone Acetyltransferases (EC 2.3.1.48) ; TATA-binding protein associated factor 250 kDa (EC 2.7.11.1)
Language	English
Publishing date	2017-09-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2720528-9
ISSN	2213-6711 ; 2213-6711
ISSN (online)	2213-6711
ISSN	2213-6711
DOI	10.1016/j.stemcr.2017.08.021
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