Changing and stable chromatin accessibility supports transcriptional overhaul during neural stem cell activation and is altered with age

LRIG1 is a gatekeeper to exit from quiescence in adult neural stem cells

(2021) María Ángeles Marqués-Torrejón et al.   Nature Communications

Vimentin Coordinates Protein Turnover at the Aggresome during Neural Stem Cell Quiescence Exit

(2020) Christopher S. Morrow et al.   Cell Stem Cell

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

(2020) Svetlana O. Dodonova et al.   NATURE

Mechanisms of enhanced quiescence in neural stem cell aging

(2020) Amanda J Audesse et al.   MECHANISMS OF AGEING AND DEVELOPMENT

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

(2020) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Adult hippocampal neurogenesis is abundant in neurologically healthy subjects and drops sharply in patients with Alzheimer’s disease

(2019) Elena P. Moreno-Jiménez et al.   NATURE MEDICINE

FOXO3 directly regulates an autophagy network to functionally regulate proteostasis in adult neural stem cells

(2019) Amanda J. Audesse et al.   PLoS Genetics

Id4 promotes the elimination of the pro-activation factor Ascl1 to maintain quiescence of adult hippocampal stem cells

(2019) Isabelle Maria Blomfield et al.   eLife

Quiescence of Adult Mammalian Neural Stem Cells: A Highly Regulated Rest

(2019) Noelia Urbán et al.   NEURON

Human Hippocampal Neurogenesis Persists throughout Aging

(2018) Maura Boldrini et al.   Cell Stem Cell

Human Adult Neurogenesis: Evidence and Remaining Questions

(2018) Gerd Kempermann et al.   Cell Stem Cell

Human hippocampal neurogenesis drops sharply in children to undetectable levels in adults

(2018) Shawn F. Sorrells et al.   NATURE

Lysosome activation clears aggregates and enhances quiescent neural stem cell activation during aging

(2018) Dena S. Leeman et al.   SCIENCE

Distinct Molecular Signatures of Quiescent and Activated Adult Neural Stem Cells Reveal Specific Interactions with Their Microenvironment

(2018) Lise Morizur et al.   Stem Cell Reports

FoxO Function Is Essential for Maintenance of Autophagic Flux and Neuronal Morphogenesis in Adult Neurogenesis

(2018) Iris Schäffner et al.   NEURON

Chromatin accessibility dynamics reveal novel functional enhancers inC. elegans

(2017) Aaron C. Daugherty et al.   GENOME RESEARCH

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

(2017) Jonathan A. Beagan et al.   GENOME RESEARCH

The chromatin accessibility signature of human immune aging stems from CD8+T cells

(2017) Duygu Ucar et al.   JOURNAL OF EXPERIMENTAL MEDICINE

CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

(2017) Tyler S Klann et al.   NATURE BIOTECHNOLOGY

Role of Mitochondrial Metabolism in the Control of Early Lineage Progression and Aging Phenotypes in Adult Hippocampal Neurogenesis

(2017) Ruth Beckervordersandforth et al.   NEURON

A Fatty Acid Oxidation-Dependent Metabolic Shift Regulates Adult Neural Stem Cell Activity

(2017) Marlen Knobloch et al.   Cell Reports

Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage

(2017) Ben W. Dulken et al.   Cell Reports

Reduced Nrf2 expression mediates the decline in neural stem cell function during a critical middle-age period

(2016) Mandi J. Corenblum et al.   AGING CELL

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Essential role of proteasomes in maintaining self-renewal in neural progenitor cells

(2016) Yunhe Zhao et al.   Scientific Reports

Age-related neurogenesis decline in the subventricular zone is associated with specific cell cycle regulation changes in activated neural stem cells

(2016) Mathieu Daynac et al.   Scientific Reports

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

(2015) Jaehoon Shin et al.   Cell Stem Cell

Adult Mammalian Neural Stem Cells and Neurogenesis: Five Decades Later

(2015) Allison M. Bond et al.   Cell Stem Cell

Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury

(2015) Enric Llorens-Bobadilla et al.   Cell Stem Cell

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Transcriptional control of stem cell fate by E2Fs and pocket proteins

(2015) Lisa M. Julian et al.   Frontiers in Genetics

GT-Scan: identifying unique genomic targets

(2014) A. O'Brien et al.   BIOINFORMATICS

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(2014) Li Shen et al.   BMC GENOMICS

Neurogenesis in the Striatum of the Adult Human Brain

(2014) Aurélie Ernst et al.   CELL

Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

(2014) Juan L. Mateo et al.   GENOME RESEARCH

Prospective Identification and Purification of Quiescent Adult Neural Stem Cells from Their In Vivo Niche

(2014) Paolo Codega et al.   NEURON

Stroke Increases Neural Stem Cells and Angiogenesis in the Neurogenic Niche of the Adult Mouse

(2014) Rui Lan Zhang et al.   PLoS One

Beyond boundaries—Eph:ephrin signaling in neurogenesis

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iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Epigenomic enhancer annotation reveals a key role for NFIX in neural stem cell quiescence

(2013) B. Martynoga et al.   GENES & DEVELOPMENT

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

FOXO3 Shares Common Targets with ASCL1 Genome-wide and Inhibits ASCL1-Dependent Neurogenesis

(2013) Ashley E. Webb et al.   Cell Reports

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Division-Coupled Astrocytic Differentiation and Age-Related Depletion of Neural Stem Cells in the Adult Hippocampus

(2011) Juan M. Encinas et al.   Cell Stem Cell

Eyes Wide Open: A Critical Review of Sphere-Formation as an Assay for Stem Cells

(2011) Erika Pastrana et al.   Cell Stem Cell

A novel function of the proneural factor Ascl1 in progenitor proliferation identified by genome-wide characterization of its targets

(2011) D. S. Castro et al.   GENES & DEVELOPMENT

Interplay between FGF2 and BMP controls the self-renewal, dormancy and differentiation of rat neural stem cells

(2011) Y. Sun et al.   JOURNAL OF CELL SCIENCE

The ageing systemic milieu negatively regulates neurogenesis and cognitive function

(2011) Saul A. Villeda et al.   NATURE

Signaling through BMPR-IA Regulates Quiescence and Long-Term Activity of Neural Stem Cells in the Adult Hippocampus

(2010) Helena Mira et al.   Cell Stem Cell

The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery

(2010) T. J. Parry et al.   GENES & DEVELOPMENT

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

FoxOs Cooperatively Regulate Diverse Pathways Governing Neural Stem Cell Homeostasis

(2009) Ji-hye Paik et al.   Cell Stem Cell

FoxO3 Regulates Neural Stem Cell Homeostasis

(2009) Valérie M. Renault et al.   Cell Stem Cell

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

AQP4 knockout impairs proliferation, migration and neuronal differentiation of adult neural stem cells

(2008) H. Kong et al.   JOURNAL OF CELL SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY