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  1. Artikel ; Online: CRISPR off-targets: a question of context.

    Haeussler, Maximilian

    Cell biology and toxicology

    2019  Band 36, Heft 1, Seite(n) 5–9

    Mesh-Begriff(e) Artifacts ; Base Pair Mismatch/genetics ; Base Pair Mismatch/physiology ; CRISPR-Cas Systems/genetics ; CRISPR-Cas Systems/physiology ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Gene Editing/ethics ; Gene Editing/methods ; Gene Editing/trends ; Humans
    Sprache Englisch
    Erscheinungsdatum 2019-11-16
    Erscheinungsland Netherlands
    Dokumenttyp Editorial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 48824-0
    ISSN 1573-6822 ; 0742-2091
    ISSN (online) 1573-6822
    ISSN 0742-2091
    DOI 10.1007/s10565-019-09497-1
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens.

    Concordet, Jean-Paul / Haeussler, Maximilian

    Nucleic acids research

    2018  Band 46, Heft W1, Seite(n) W242–W245

    Abstract: CRISPOR.org is a web tool for genome editing experiments with the CRISPR-Cas9 system. It finds guide RNAs in an input sequence and ranks them according to different scores that evaluate potential off-targets in the genome of interest and predict on- ... ...

    Abstract CRISPOR.org is a web tool for genome editing experiments with the CRISPR-Cas9 system. It finds guide RNAs in an input sequence and ranks them according to different scores that evaluate potential off-targets in the genome of interest and predict on-target activity. The list of genomes is continuously expanded, with more 150 genomes added in the last two years. CRISPOR tries to provide a comprehensive solution from selection, cloning and expression of guide RNA as well as providing primers needed for testing guide activity and potential off-targets. Recent developments include batch design for genome-wide CRISPR and saturation screens, creating custom oligonucleotides for guide cloning and the design of next generation sequencing primers to test for off-target mutations. CRISPOR is available from http://crispor.org, including the full source code of the website and a stand-alone, command-line version.
    Mesh-Begriff(e) Base Sequence ; CRISPR-Associated Protein 9 ; CRISPR-Cas Systems ; Gene Editing ; Gene Knockout Techniques ; Genome ; Internet ; Mutagenesis ; Oligonucleotides ; RNA/chemistry ; Software ; Workflow
    Chemische Substanzen Oligonucleotides ; RNA (63231-63-0) ; CRISPR-Associated Protein 9 (EC 3.1.-)
    Sprache Englisch
    Erscheinungsdatum 2018-05-14
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gky354
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: A Meta-Atlas of the Developing Human Cortex Identifies Modules Driving Cell Subtype Specification.

    Nano, Patricia R / Fazzari, Elisa / Azizad, Daria / Nguyen, Claudia V / Wang, Sean / Kan, Ryan L / Wick, Brittney / Haeussler, Maximilian / Bhaduri, Aparna

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Human brain development requires the generation of hundreds of diverse cell types, a process targeted by recent single-cell transcriptomic profiling efforts. Through a meta-analysis of seven of these published datasets, we have generated 225 meta-modules ...

    Abstract Human brain development requires the generation of hundreds of diverse cell types, a process targeted by recent single-cell transcriptomic profiling efforts. Through a meta-analysis of seven of these published datasets, we have generated 225 meta-modules - gene co-expression networks that can describe mechanisms underlying cortical development. Several meta-modules have potential roles in both establishing and refining cortical cell type identities, and we validated their spatiotemporal expression in primary human cortical tissues. These include meta-module 20, associated with FEZF2+ deep layer neurons. Half of meta-module 20 genes are putative FEZF2 targets, including TSHZ3, a transcription factor associated with neurodevelopmental disorders. Human cortical organoid experiments validated that both factors are necessary for deep layer neuron specification. Importantly, subtle manipulations of these factors drive slight changes in meta-module activity that cascade into strong differences in cell fate - demonstrating how of our meta-atlas can engender further mechanistic analyses of cortical fate specification.
    Sprache Englisch
    Erscheinungsdatum 2023-09-13
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.09.12.557406
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel: A Panoramic View of Cell Population Dynamics in Mammalian Aging.

    Zhang, Zehao / Schaefer, Chloe / Jiang, Weirong / Lu, Ziyu / Lee, Jasper / Sziraki, Andras / Abdulraouf, Abdulraouf / Wick, Brittney / Haeussler, Maximilian / Li, Zhuoyan / Molla, Gesmira / Satija, Rahul / Zhou, Wei / Cao, Junyue

    bioRxiv : the preprint server for biology

    2024  

    Abstract: To elucidate the aging-associated cellular population dynamics throughout the body, here we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissue samples, encompassing a range of organs across different ... ...

    Abstract To elucidate the aging-associated cellular population dynamics throughout the body, here we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissue samples, encompassing a range of organs across different life stages, sexes, and genotypes. This comprehensive dataset allowed us to identify more than 3,000 unique cellular states and catalog over 200 distinct aging-associated cell populations experiencing significant depletion or expansion. Our panoramic analysis uncovered temporally structured, organ- and lineage-specific shifts of cellular dynamics during lifespan progression. Moreover, we investigated aging-associated alterations in immune cell populations, revealing both widespread shifts and organ-specific changes. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte-dependent. The breadth and depth of our 'cell-omics' methodology not only enhance our comprehension of cellular aging but also lay the groundwork for exploring the complex regulatory networks among varied cell types in the context of aging and aging-associated diseases.
    Sprache Englisch
    Erscheinungsdatum 2024-03-05
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2024.03.01.583001
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel: Genome Editing with CRISPR-Cas9: Can It Get Any Better?

    Haeussler, Maximilian / Concordet, Jean-Paul

    Journal of genetics and genomics = Yi chuan xue bao

    2016  Band 43, Heft 5, Seite(n) 239–250

    Abstract: The CRISPR-Cas revolution is taking place in virtually all fields of life sciences. Harnessing DNA cleavage with the CRISPR-Cas9 system of Streptococcus pyogenes has proven to be extraordinarily simple and efficient, relying only on the design of a ... ...

    Abstract The CRISPR-Cas revolution is taking place in virtually all fields of life sciences. Harnessing DNA cleavage with the CRISPR-Cas9 system of Streptococcus pyogenes has proven to be extraordinarily simple and efficient, relying only on the design of a synthetic single guide RNA (sgRNA) and its co-expression with Cas9. Here, we review the progress in the design of sgRNA from the original dual RNA guide for S. pyogenes and Staphylococcus aureus Cas9 (SpCas9 and SaCas9). New assays for genome-wide identification of off-targets have provided important insights into the issue of cleavage specificity in vivo. At the same time, the on-target activity of thousands of guides has been determined. These data have led to numerous online tools that facilitate the selection of guide RNAs in target sequences. It appears that for most basic research applications, cleavage activity can be maximized and off-targets minimized by carefully choosing guide RNAs based on computational predictions. Moreover, recent studies of Cas proteins have further improved the flexibility and precision of the CRISPR-Cas toolkit for genome editing. Inspired by the crystal structure of the complex of sgRNA-SpCas9 bound to target DNA, several variants of SpCas9 have recently been engineered, either with novel protospacer adjacent motifs (PAMs) or with drastically reduced off-targets. Novel Cas9 and Cas9-like proteins called Cpf1 have also been characterized from other bacteria and will benefit from the insights obtained from SpCas9. Genome editing with CRISPR-Cas9 may also progress with better understanding and control of cellular DNA repair pathways activated after Cas9-induced DNA cleavage.
    Mesh-Begriff(e) Animals ; Base Sequence ; CRISPR-Cas Systems/genetics ; Gene Editing/methods ; Gene Knockout Techniques ; Genomics/methods ; Humans ; RNA, Guide, CRISPR-Cas Systems/genetics
    Chemische Substanzen RNA, Guide, CRISPR-Cas Systems
    Sprache Englisch
    Erscheinungsdatum 2016-04-24
    Erscheinungsland China
    Dokumenttyp Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2374568-X
    ISSN 1873-5533 ; 1673-8527
    ISSN (online) 1873-5533
    ISSN 1673-8527
    DOI 10.1016/j.jgg.2016.04.008
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel: Genome Editing with CRISPR-Cas9: Can It Get Any Better?

    Haeussler, Maximilian / Jean-Paul Concordet

    Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China Journal of genetics and genomics. 2016 May 20, v. 43, no. 5

    2016  

    Abstract: The CRISPR-Cas revolution is taking place in virtually all fields of life sciences. Harnessing DNA cleavage with the CRISPR-Cas9 system of Streptococcus pyogenes has proven to be extraordinarily simple and efficient, relying only on the design of a ... ...

    Abstract The CRISPR-Cas revolution is taking place in virtually all fields of life sciences. Harnessing DNA cleavage with the CRISPR-Cas9 system of Streptococcus pyogenes has proven to be extraordinarily simple and efficient, relying only on the design of a synthetic single guide RNA (sgRNA) and its co-expression with Cas9. Here, we review the progress in the design of sgRNA from the original dual RNA guide for S. pyogenes and Staphylococcus aureus Cas9 (SpCas9 and SaCas9). New assays for genome-wide identification of off-targets have provided important insights into the issue of cleavage specificity in vivo. At the same time, the on-target activity of thousands of guides has been determined. These data have led to numerous online tools that facilitate the selection of guide RNAs in target sequences. It appears that for most basic research applications, cleavage activity can be maximized and off-targets minimized by carefully choosing guide RNAs based on computational predictions. Moreover, recent studies of Cas proteins have further improved the flexibility and precision of the CRISPR-Cas toolkit for genome editing. Inspired by the crystal structure of the complex of sgRNA-SpCas9 bound to target DNA, several variants of SpCas9 have recently been engineered, either with novel protospacer adjacent motifs (PAMs) or with drastically reduced off-targets. Novel Cas9 and Cas9-like proteins called Cpf1 have also been characterized from other bacteria and will benefit from the insights obtained from SpCas9. Genome editing with CRISPR-Cas9 may also progress with better understanding and control of cellular DNA repair pathways activated after Cas9-induced DNA cleavage.
    Schlagwörter bacteria ; computer software ; crystal structure ; DNA ; DNA damage ; DNA repair ; genome ; prediction ; proteins ; RNA ; Staphylococcus aureus ; Streptococcus pyogenes
    Sprache Englisch
    Erscheinungsverlauf 2016-0520
    Umfang p. 239-250.
    Erscheinungsort Elsevier Ltd
    Dokumenttyp Artikel
    ZDB-ID 2374568-X
    ISSN 1873-5533 ; 1673-8527
    ISSN (online) 1873-5533
    ISSN 1673-8527
    DOI 10.1016/j.jgg.2016.04.008
    Datenquelle NAL Katalog (AGRICOLA)

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  7. Artikel ; Online: Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia.

    Eze, Ugomma C / Bhaduri, Aparna / Haeussler, Maximilian / Nowakowski, Tomasz J / Kriegstein, Arnold R

    Nature neuroscience

    2021  Band 24, Heft 4, Seite(n) 584–594

    Abstract: The human cortex comprises diverse cell types that emerge from an initially uniform neuroepithelium that gives rise to radial glia, the neural stem cells of the cortex. To characterize the earliest stages of human brain development, we performed single- ... ...

    Abstract The human cortex comprises diverse cell types that emerge from an initially uniform neuroepithelium that gives rise to radial glia, the neural stem cells of the cortex. To characterize the earliest stages of human brain development, we performed single-cell RNA-sequencing across regions of the developing human brain, including the telencephalon, diencephalon, midbrain, hindbrain and cerebellum. We identify nine progenitor populations physically proximal to the telencephalon, suggesting more heterogeneity than previously described, including a highly prevalent mesenchymal-like population that disappears once neurogenesis begins. Comparison of human and mouse progenitor populations at corresponding stages identifies two progenitor clusters that are enriched in the early stages of human cortical development. We also find that organoid systems display low fidelity to neuroepithelial and early radial glia cell types, but improve as neurogenesis progresses. Overall, we provide a comprehensive molecular and spatial atlas of early stages of human brain and cortical development.
    Mesh-Begriff(e) Animals ; Cerebral Cortex/cytology ; Cerebral Cortex/embryology ; Ependymoglial Cells/cytology ; Humans ; Neural Stem Cells/cytology ; Neuroepithelial Cells/cytology ; Neurogenesis ; Single-Cell Analysis
    Sprache Englisch
    Erscheinungsdatum 2021-03-15
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1420596-8
    ISSN 1546-1726 ; 1097-6256
    ISSN (online) 1546-1726
    ISSN 1097-6256
    DOI 10.1038/s41593-020-00794-1
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel: Single cell analysis of dup15q syndrome reveals developmental and postnatal molecular changes in autism.

    Perez, Yonatan / Velmeshev, Dmitry / Wang, Li / White, Matthew / Siebert, Clara / Baltazar, Jennifer / Dutton, Natalia Garcia / Wang, Shaohui / Haeussler, Maximilian / Chamberlain, Stormy / Kriegstein, Arnold

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Duplication 15q (dup15q) syndrome is the most common genetic cause of autism spectrum disorder (ASD). Due to a higher genetic and phenotypic homogeneity compared to idiopathic autism, dup15q syndrome provides a well-defined setting to investigate ASD ... ...

    Abstract Duplication 15q (dup15q) syndrome is the most common genetic cause of autism spectrum disorder (ASD). Due to a higher genetic and phenotypic homogeneity compared to idiopathic autism, dup15q syndrome provides a well-defined setting to investigate ASD mechanisms. Previous bulk gene expression studies identified shared molecular changes in ASD. However, how cell type specific changes compare across different autism subtypes and how they change during development is largely unknown. In this study, we used single cell and single nucleus mRNA sequencing of dup15q cortical organoids from patient iPSCs, as well as post-mortem patient brain samples. We find cell-type specific dysregulated programs that underlie dup15q pathogenesis, which we validate by spatial resolved transcriptomics using brain tissue samples. We find degraded identity and vulnerability of deep-layer neurons in fetal stage organoids and highlight increased molecular burden of postmortem upper-layer neurons implicated in synaptic signaling, a finding shared between idiopathic ASD and dup15q syndrome. Gene co-expression network analysis of organoid and postmortem excitatory neurons uncovers modules enriched with autism risk genes. Organoid developmental modules were involved in transcription regulation via chromatin remodeling, while postmortem modules were associated with synaptic transmission and plasticity. The findings reveal a shifting landscape of ASD cellular vulnerability during brain development.
    Sprache Englisch
    Erscheinungsdatum 2023-09-22
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.09.22.559056
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: The dynseq browser track shows context-specific features at nucleotide resolution.

    Nair, Surag / Barrett, Arjun / Li, Daofeng / Raney, Brian J / Lee, Brian T / Kerpedjiev, Peter / Ramalingam, Vivekanandan / Pampari, Anusri / Lekschas, Fritz / Wang, Ting / Haeussler, Maximilian / Kundaje, Anshul

    Nature genetics

    2022  Band 54, Heft 11, Seite(n) 1581–1583

    Mesh-Begriff(e) Nucleotides ; Software ; Databases, Genetic ; Internet ; Web Browser
    Chemische Substanzen Nucleotides
    Sprache Englisch
    Erscheinungsdatum 2022-10-31
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-022-01194-w
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel ; Online: Cross-regional homeostatic and reactive glial signatures in multiple sclerosis.

    Trobisch, Tim / Zulji, Amel / Stevens, Nikolas A / Schwarz, Sophia / Wischnewski, Sven / Öztürk, Mikail / Perales-Patón, Javier / Haeussler, Maximilian / Saez-Rodriguez, Julio / Velmeshev, Dmitry / Schirmer, Lucas

    Acta neuropathologica

    2022  Band 144, Heft 5, Seite(n) 987–1003

    Abstract: Multiple sclerosis (MS) is a multifocal and progressive inflammatory disease of the central nervous system (CNS). However, the compartmentalized pathology of the disease affecting various anatomical regions including gray and white matter and lack of ... ...

    Abstract Multiple sclerosis (MS) is a multifocal and progressive inflammatory disease of the central nervous system (CNS). However, the compartmentalized pathology of the disease affecting various anatomical regions including gray and white matter and lack of appropriate disease models impede understanding of the disease. Utilizing single-nucleus RNA-sequencing and multiplex spatial RNA mapping, we generated an integrated transcriptomic map comprising leukocortical, cerebellar and spinal cord areas in normal and MS tissues that captures regional subtype diversity of various cell types with an emphasis on astrocytes and oligodendrocytes. While we found strong cross-regional diversity among glial subtypes in control tissue, regional signatures become more obscure in MS. This suggests that patterns of transcriptomic changes in MS are shared across regions and converge on specific pathways, especially those regulating cellular stress and immune activation. In addition, we found evidence that a subtype of white matter oligodendrocytes appearing across all three CNS regions adopt pro-remyelinating gene signatures in MS. In summary, our data suggest that cross-regional transcriptomic glial signatures overlap in MS, with different reactive glial cell types capable of either exacerbating or ameliorating pathology.
    Mesh-Begriff(e) Astrocytes/pathology ; Humans ; Multiple Sclerosis/pathology ; Neuroglia/pathology ; Oligodendroglia/metabolism ; RNA/metabolism ; White Matter/pathology
    Chemische Substanzen RNA (63231-63-0)
    Sprache Englisch
    Erscheinungsdatum 2022-09-16
    Erscheinungsland Germany
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1079-0
    ISSN 1432-0533 ; 0001-6322
    ISSN (online) 1432-0533
    ISSN 0001-6322
    DOI 10.1007/s00401-022-02497-2
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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