Vivek Nandakumar

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian et autres

In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in …

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Author Correction: Perspectives on ENCODE

Federi Bronwen co Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian et autres

In this Article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE …

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Enhanced HbF reactivation by multiplex mutagenesis of thalassemic CD34+ cells in vitro and in vivo

Nikoletta Psatha, Chang Li, Vivek Nandakumar, Grigorios Georgolopoulos et autres

Thalassemia or sickle cell patients with hereditary persistence of fetal hemoglobin (HbF) have an ameliorated clinical phenotype and, in some cases, can achieve transfusion independence. Inactivation via genome editing of γ-globin developmental suppressors, such as BCL11A or LRF/ZBTB7A, or of their binding …

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Abstract PO-048: Visual nucleotyping identifies chromatin phenotypes triggered by genome editing

Vivek Nandakumar, Sandra Stehling-Sun, William Kerwin, Alister P. W. Funnell et autres

Abstract Optical microscopy has the potential to provide rapid phenotypic readout of cellular states. Here we show that automated optical phenotyping of nuclei is capable of rapidly and reliably discriminating the effects of targeted mutations to chromatin remodelers, which are major players …

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Perspectives on ENCODE

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian et autres

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open …

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Expanded encyclopaedias of DNA elements in the human and mouse genomes

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Veena Afzal et autres

Abstract The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis …

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Drosophila Wash and the Wash regulatory complex function in nuclear envelope budding

Jeffrey M. Verboon, Mitsutoshi Nakamura, Kerri Davidson, Jacob R. Decker et autres

ABSTRACT Nuclear envelope (NE) budding is a recently described phenomenon wherein large macromolecular complexes are packaged inside the nucleus and extruded through the nuclear membranes. Although a general outline of the cellular events occurring during NE budding is now in place, little …

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Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling

John Lazar, Sandra Stehling-Sun, Vivek Nandakumar, Hao Wang et autres

(Cell Reports 31, 107676-1–107676-16.e1–e5; May 26, 2020) In the originally published version of this article, the order of authors in the author list was incorrect. The last two authors on the list should be, in this order: John A. Stamatoyannopoulos and Alister …

Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling

John Lazar, Sandra Stehling-Sun, Vivek Nandakumar, Hao Wang et autres

The human genome encodes millions of regulatory elements, of which only a small fraction are active within a given cell type. Little is known about the global impact of chromatin remodelers on regulatory DNA landscapes and how this translates to gene expression. …

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Promoter keyholes enable specific and persistent multi-gene expression programs in primary T cells without genome modification

Matthew S. Wilken, Christie Ciarlo, Jocelynn R. Pearl, Jordan Bloom et autres

Non-invasive epigenome editing is a promising strategy for engineering gene expression programs, yet potency, specificity, and persistence remain challenging. Here we show that effective epigenome editing is gated at single-base precision via 'keyhole' sites in endogenous regulatory DNA. Synthetic repressors targeting promoter …

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Quantitative dialing of gene expression via precision targeting of KRAB repressor

Matthew S. Wilken, Christie Ciarlo, Jocelynn R. Pearl, Elaine Schanzer et autres

Abstract Human genes are regulated quantitatively, yet the ability to specify the expression level of a native gene accurately and specifically using a defined reagent has remained elusive. Here we show that precise targeting of KRAB repressive domain within regulatory DNA unlocks …

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Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins

Alexander Federation, Vivek Nandakumar, Brian C. Searle, Andrew B. Stergachis et autres

Transcription factors and other chromatin-associated proteins are difficult to quantify comprehensively. Here, we combine facile nuclear sub-fractionation with data-independent acquisition mass spectrometry to achieve rapid, sensitive, and highly parallel quantification of the nuclear proteome in human cells. We apply this approach to …

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