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  1. No Access

    Article

    The three-dimensional landscape of cortical chromatin accessibility in Alzheimer’s disease

    To characterize the dysregulation of chromatin accessibility in Alzheimer’s disease (AD), we generated 636 ATAC-seq libraries from neuronal and nonneuronal nuclei isolated from the superior temporal gyrus and ...

    Jaroslav Bendl, Mads E. Hauberg, Kiran Girdhar, Eunju Im… in Nature Neuroscience (2022)

  2. No Access

    Article

    Population-level variation in enhancer expression identifies disease mechanisms in the human brain

    Identification of risk variants for neuropsychiatric diseases within enhancers underscores the importance of understanding population-level variation in enhancer function in the human brain. Besides regulating...

    Pengfei Dong, Gabriel E. Hoffman, Pasha Apontes, Jaroslav Bendl… in Nature Genetics (2022)

  3. No Access

    Article

    Genetics of the human microglia regulome refines Alzheimer’s disease risk loci

    Microglia are brain myeloid cells that play a critical role in neuroimmunity and the etiology of Alzheimer’s disease (AD), yet our understanding of how the genetic regulatory landscape controls microglial func...

    Roman Kosoy, John F. Fullard, Biao Zeng, Jaroslav Bendl, Pengfei Dong… in Nature Genetics (2022)

  4. No Access

    Article

    Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains

    Chromosomal organization, scaling from the 147-base pair (bp) nucleosome to megabase-ranging domains encompassing multiple transcriptional units, including heritability loci for psychiatric traits, remains lar...

    Kiran Girdhar, Gabriel E. Hoffman, Jaroslav Bendl, Samir Rahman… in Nature Neuroscience (2022)

  5. No Access

    Chapter

    Genetic Variation in Long-Range Enhancers

    Cis-regulatory elements (CREs), including insulators, promoters, and enhancers, play critical roles in the establishment and maintenance of normal cellular function. Within each cell, the 3D structure of chromati...

    John F. Fullard, Samir Rahman, Panos Roussos in Behavioral Neurogenomics (2019)

  6. No Access

    Protocol

    Measuring mRNA Decay in Budding Yeast Using Single Molecule FISH

    Cellular mRNA levels are determined by the rates of mRNA synthesis and mRNA decay. Typically, mRNA degradation kinetics are measured on a population of cells that are either chemically treated or genetically e...

    Tatjana Trcek, Samir Rahman, Daniel Zenklusen in mRNA Decay (2018)

  7. No Access

    Article

    Bimodal expression of PHO84 is modulated by early termination of antisense transcription

    The presence of PHO84 sense and antisense transcripts in single cells is strongly anticorrelated, suggesting a switch-like regulation mechanism. Data from single-molecule fluorescent in situ hybridization experim...

    Manuele Castelnuovo, Samir Rahman, Elisa Guffanti… in Nature Structural & Molecular Biology (2013)

  8. No Access

    Protocol

    Single-Molecule Resolution Fluorescent In Situ Hybridization (smFISH) in the Yeast S. cerevisiae

    Regulating gene expression is a major task for all cellular systems. RNA production and degradation plays a critical role in this process and accurately measuring cellular mRNA levels is essential to understan...

    Samir Rahman, Daniel Zenklusen in Imaging Gene Expression (2013)