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Article ; Online: Synthetic reversed sequences reveal default genomic states.

Camellato, Brendan R / Brosh, Ran / Ashe, Hannah J / Maurano, Matthew T / Boeke, Jef D

2024 Volume 628, Issue 8007, Page(s) 373–380

Abstract: Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or 'noise' ...

Abstract	Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or 'noise'
MeSH term(s)	Animals ; Humans ; Mice ; Chromatin/genetics ; CpG Islands ; Genes, Synthetic/genetics ; Genome/genetics ; Mouse Embryonic Stem Cells/metabolism ; Promoter Regions, Genetic/genetics ; Saccharomyces cerevisiae/genetics ; Transcription, Genetic ; Hypoxanthine Phosphoribosyltransferase/genetics ; Evolution, Molecular
Chemical Substances	Chromatin ; Hypoxanthine Phosphoribosyltransferase (EC 2.4.2.8)
Language	English
Publishing date	2024-03-06
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-024-07128-2
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Zs.A 26: 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: Author Correction: Longitudinal scRNA-seq analysis in mouse and human informs optimization of rapid mouse astrocyte differentiation protocols.

Frazel, Paul W / Labib, David / Fisher, Theodore / Brosh, Ran / Pirjanian, Nicolette / Marchildon, Anne / Boeke, Jef D / Fossati, Valentina / Liddelow, Shane A

Nature neuroscience

2023 Volume 27, Issue 1, Page(s) 209

Language	English
Publishing date	2023-11-23
Publishing country	United States
Document type	Published Erratum
ZDB-ID	1420596-8
ISSN	1546-1726 ; 1097-6256
ISSN (online)	1546-1726
ISSN	1097-6256
DOI	10.1038/s41593-023-01531-0
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Zs.A 4891: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 67: Show issues

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Article: Genomic context sensitizes regulatory elements to genetic disruption.

Ordoñez, Raquel / Zhang, Weimin / Ellis, Gwen / Zhu, Yinan / Ashe, Hannah J / Ribeiro-Dos-Santos, André M / Brosh, Ran / Huang, Emily / Hogan, Megan S / Boeke, Jef D / Maurano, Matthew T

bioRxiv : the preprint server for biology

2024

Abstract: Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis. Thus it remains unclear to what extent enhancer function at native loci relies on surrounding genomic context. Using the Big-IN technology ...

Abstract	Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis. Thus it remains unclear to what extent enhancer function at native loci relies on surrounding genomic context. Using the Big-IN technology for targeted integration of large DNAs, we analyzed the regulatory architecture of the murine
Language	English
Publishing date	2024-03-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.02.547201
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Article ; Online: Genomic context sensitivity of insulator function.

Ribeiro-Dos-Santos, André M / Hogan, Megan S / Luther, Raven D / Brosh, Ran / Maurano, Matthew T

Genome research

2022 Volume 32, Issue 3, Page(s) 425–436

Abstract: The specificity of interactions between genomic regulatory elements and potential target genes is influenced by the binding of insulator proteins such as CTCF, which can act as potent enhancer blockers when interposed between an enhancer and a promoter ... ...

Abstract	The specificity of interactions between genomic regulatory elements and potential target genes is influenced by the binding of insulator proteins such as CTCF, which can act as potent enhancer blockers when interposed between an enhancer and a promoter in a reporter assay. But not all CTCF sites genome-wide function as insulator elements, depending on cellular and genomic context. To dissect the influence of genomic context on enhancer blocker activity, we integrated reporter constructs with promoter-only, promoter and enhancer, and enhancer blocker configurations at hundreds of thousands of genomic sites using the
MeSH term(s)	CCCTC-Binding Factor/genetics ; CCCTC-Binding Factor/metabolism ; Enhancer Elements, Genetic ; Genomics ; Insulator Elements ; Promoter Regions, Genetic
Chemical Substances	CCCTC-Binding Factor
Language	English
Publishing date	2022-01-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.276449.121
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Zs.A 3729: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 8: Show issues

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Article ; Online: CREEPY: CRISPR-mediated editing of synthetic episomes in yeast.

Zhao, Yu / Coelho, Camila / Lauer, Stephanie / Majewski, Miłosz / Laurent, Jon M / Brosh, Ran / Boeke, Jef D

Nucleic acids research

2023 Volume 51, Issue 13, Page(s) e72

Abstract: Use of synthetic genomics to design and build 'big' DNA has revolutionized our ability to answer fundamental biological questions by employing a bottom-up approach. Saccharomyces cerevisiae, or budding yeast, has become the major platform to assemble ... ...

Abstract	Use of synthetic genomics to design and build 'big' DNA has revolutionized our ability to answer fundamental biological questions by employing a bottom-up approach. Saccharomyces cerevisiae, or budding yeast, has become the major platform to assemble large synthetic constructs thanks to its powerful homologous recombination machinery and the availability of well-established molecular biology techniques. However, introducing designer variations to episomal assemblies with high efficiency and fidelity remains challenging. Here we describe CRISPR Engineering of EPisomes in Yeast, or CREEPY, a method for rapid engineering of large synthetic episomal DNA constructs. We demonstrate that CRISPR editing of circular episomes presents unique challenges compared to modifying native yeast chromosomes. We optimize CREEPY for efficient and precise multiplex editing of >100 kb yeast episomes, providing an expanded toolkit for synthetic genomics.
MeSH term(s)	Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; CRISPR-Cas Systems/genetics ; DNA ; Gene Editing/methods ; Plasmids/genetics ; Yeasts/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-06-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
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/gkad491
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Article ; Online: Longitudinal scRNA-seq analysis in mouse and human informs optimization of rapid mouse astrocyte differentiation protocols.

Frazel, Paul W / Labib, David / Fisher, Theodore / Brosh, Ran / Pirjanian, Nicolette / Marchildon, Anne / Boeke, Jef D / Fossati, Valentina / Liddelow, Shane A

Nature neuroscience

2023 Volume 26, Issue 10, Page(s) 1726–1738

Abstract: Macroglia (astrocytes and oligodendrocytes) are required for normal development and function of the central nervous system, yet many questions remain about their emergence during the development of the brain and spinal cord. Here we used single-cell/ ... ...

Abstract	Macroglia (astrocytes and oligodendrocytes) are required for normal development and function of the central nervous system, yet many questions remain about their emergence during the development of the brain and spinal cord. Here we used single-cell/single-nucleus RNA sequencing (scRNA-seq/snRNA-seq) to analyze over 298,000 cells and nuclei during macroglia differentiation from mouse embryonic and human-induced pluripotent stem cells. We computationally identify candidate genes involved in the fate specification of glia in both species and report heterogeneous expression of astrocyte surface markers across differentiating cells. We then used our transcriptomic data to optimize a previous mouse astrocyte differentiation protocol, decreasing the overall protocol length and complexity. Finally, we used multi-omic, dual single-nuclei (sn)RNA-seq/snATAC-seq analysis to uncover potential genomic regulatory sites mediating glial differentiation. These datasets will enable future optimization of glial differentiation protocols and provide insight into human glial differentiation.
MeSH term(s)	Humans ; Mice ; Animals ; Astrocytes ; Single-Cell Gene Expression Analysis ; Cell Differentiation/genetics ; Neurogenesis ; Neuroglia ; Single-Cell Analysis/methods ; Sequence Analysis, RNA/methods
Language	English
Publishing date	2023-09-11
Publishing country	United States
Document type	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/s41593-023-01424-2
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Zs.A 4891: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article: Collagenase Administration into Periodontal Ligament Reduces the Forces Required for Tooth Extraction in an Ex situ Porcine Jaw Model.

Tohar, Ran / Alali, Hen / Ansbacher, Tamar / Brosh, Tamar / Sher, Inbal / Gafni, Yossi / Weinberg, Evgeny / Gal, Maayan

Journal of functional biomaterials

2022 Volume 13, Issue 2

Abstract: Minimally invasive exodontia is among the long-sought-for development aims of safe dental medicine. In this paper, we aim, for the first time, to examine whether the enzymatic disruption of the periodontal ligament fibers reduces the force required for ... ...

Abstract	Minimally invasive exodontia is among the long-sought-for development aims of safe dental medicine. In this paper, we aim, for the first time, to examine whether the enzymatic disruption of the periodontal ligament fibers reduces the force required for tooth extraction. To this end, recombinantly expressed clostridial collagenase G variant purified from Escherichia coli was injected into the periodontal ligament of mesial and distal roots of the first and second split porcine mandibular premolars. The vehicle solution was injected into the corresponding roots on the contralateral side. Following sixteen hours, the treated mandibles were mounted on a loading machine to measure the extraction force. In addition, the effect of the enzyme on the viability of different cell types was evaluated. An average reduction of 20% in the applied force (albeit with a large variability of 50 to 370 newton) was observed for the enzymatically treated roots, reaching up to 50% reduction in some cases. Importantly, the enzyme showed only a minor and transient effect on cellular viability, without any signs of toxicity. Using an innovative model enabling the analytical measurement of extraction forces, we show, for the first time, that the enzymatic disruption of periodontal ligament fibers substantially reduces the force required for tooth extraction. This novel technique brings us closer to atraumatic exodontia, potentially reducing intra- and post-operative complications and facilitating subsequent implant placement. The development of novel enzymes with enhanced activity may further simplify the tooth extraction process and present additional clinical relevance for the broad range of implications in the oral cavity.
Language	English
Publishing date	2022-06-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2648525-4
ISSN	2079-4983
ISSN	2079-4983
DOI	10.3390/jfb13020076
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Article ; Online: Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus.

Brosh, Ran / Coelho, Camila / Ribeiro-Dos-Santos, André M / Ellis, Gwen / Hogan, Megan S / Ashe, Hannah J / Somogyi, Nicolette / Ordoñez, Raquel / Luther, Raven D / Huang, Emily / Boeke, Jef D / Maurano, Matthew T

Molecular cell

2023 Volume 83, Issue 7, Page(s) 1140–1152.e7

Abstract: Sox2 expression in mouse embryonic stem cells (mESCs) depends on a distal cluster of DNase I hypersensitive sites (DHSs), but their individual contributions and degree of interdependence remain a mystery. We analyzed the endogenous Sox2 locus using Big- ... ...

Abstract	Sox2 expression in mouse embryonic stem cells (mESCs) depends on a distal cluster of DNase I hypersensitive sites (DHSs), but their individual contributions and degree of interdependence remain a mystery. We analyzed the endogenous Sox2 locus using Big-IN to scarlessly integrate large DNA payloads incorporating deletions, rearrangements, and inversions affecting single or multiple DHSs, as well as surgical alterations to transcription factor (TF) recognition sequences. Multiple mESC clones were derived for each payload, sequence-verified, and analyzed for Sox2 expression. We found that two DHSs comprising a handful of key TF recognition sequences were each sufficient for long-range activation of Sox2 expression. By contrast, three nearby DHSs were entirely context dependent, showing no activity alone but dramatically augmenting the activity of the autonomous DHSs. Our results highlight the role of context in modulating genomic regulatory element function, and our synthetic regulatory genomics approach provides a roadmap for the dissection of other genomic loci.
MeSH term(s)	Animals ; Mice ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Genomics ; Regulatory Sequences, Nucleic Acid/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism ; SOXB1 Transcription Factors/metabolism
Chemical Substances	di-n-hexyl sulfosuccinate (1CYC51DFL6) ; Transcription Factors ; SOXB1 Transcription Factors
Language	English
Publishing date	2023-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.02.027
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Article ; Online: Regulatory architecture of housekeeping genes is driven by promoter assemblies.

Dejosez, Marion / Dall'Agnese, Alessandra / Ramamoorthy, Mahesh / Platt, Jesse / Yin, Xing / Hogan, Megan / Brosh, Ran / Weintraub, Abraham S / Hnisz, Denes / Abraham, Brian J / Young, Richard A / Zwaka, Thomas P

Cell reports

2023 Volume 42, Issue 5, Page(s) 112505

Abstract: Genes that are key to cell identity are generally regulated by cell-type-specific enhancer elements bound by transcription factors, some of which facilitate looping to distant gene promoters. In contrast, genes that encode housekeeping functions, whose ... ...

Abstract	Genes that are key to cell identity are generally regulated by cell-type-specific enhancer elements bound by transcription factors, some of which facilitate looping to distant gene promoters. In contrast, genes that encode housekeeping functions, whose regulation is essential for normal cell metabolism and growth, generally lack interactions with distal enhancers. We find that Ronin (Thap11) assembles multiple promoters of housekeeping and metabolic genes to regulate gene expression. This behavior is analogous to how enhancers are brought together with promoters to regulate cell identity genes. Thus, Ronin-dependent promoter assemblies provide a mechanism to explain why housekeeping genes can forgo distal enhancer elements and why Ronin is important for cellular metabolism and growth control. We propose that clustering of regulatory elements is a mechanism common to cell identity and housekeeping genes but is accomplished by different factors binding distinct control elements to establish enhancer-promoter or promoter-promoter interactions, respectively.
MeSH term(s)	Genes, Essential/genetics ; Enhancer Elements, Genetic/genetics ; Transcription Factors/metabolism ; Promoter Regions, Genetic/genetics
Chemical Substances	Transcription Factors
Language	English
Publishing date	2023-05-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2023.112505
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Article ; Online: On the genetic basis of tail-loss evolution in humans and apes.

Nature

2024 Volume 626, Issue 8001, Page(s) 1042–1048

Abstract: The loss of the tail is among the most notable anatomical changes to have occurred along the evolutionary lineage leading to humans and to the 'anthropomorphous apes' ...

Abstract	The loss of the tail is among the most notable anatomical changes to have occurred along the evolutionary lineage leading to humans and to the 'anthropomorphous apes'
MeSH term(s)	Animals ; Humans ; Mice ; Alternative Splicing/genetics ; Alu Elements/genetics ; Disease Models, Animal ; Evolution, Molecular ; Genome/genetics ; Hominidae/anatomy & histology ; Hominidae/genetics ; Introns/genetics ; Neural Tube Defects/genetics ; Neural Tube Defects/metabolism ; Phenotype ; Protein Isoforms/deficiency ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; T-Box Domain Proteins/deficiency ; T-Box Domain Proteins/genetics ; T-Box Domain Proteins/metabolism ; Tail/anatomy & histology ; Tail/embryology ; Exons/genetics
Chemical Substances	Protein Isoforms ; T-Box Domain Proteins ; TBXT protein, human
Language	English
Publishing date	2024-02-28
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-024-07095-8
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