Guest Editors
Rochelle Coulson
Stanford University
<p>Dr. Rochelle Coulson obtained her PhD in Integrative Genetics and Genomics from the University of California, Davis, where she studied in the lab of Dr. Janine LaSalle. Her thesis work focused on the role of the Prader-Willi locus long non-coding RNA <em>Snord116</em> in regulating local chromatin dynamics and genome-wide DNA methylation, including diurnal epigenetic rhythms. She is currently a postdoctoral scholar at Stanford University, in the labs of Dr. Philippe Mourrain and Dr. Gordon Wang, where she studies molecular and cellular pathway regulation at the synapse in Fragile X syndrome.</p>
Yihui Zhu
10x Genomics
<p>Dr. Yihui Zhu received her PhD in Integrative Genetics and Genomics with the Designated Emphasis in Biotechnology at the University of California, Davis. Her dissertation research investigated perinatal epigenetics signatures of Autism Spectrum Disorder (ASD) including the identification and initial characterization of a novel environmentally responsive ASD risk gene, <em>NHIP</em> relevant to brain development in a hitherto under-characterized region, 22q13.33 of the human genome using placenta methylome. She is currently a Scientist, Applied Bioinformatics at 10x Genomics, where she experiences analyzing data from single-cell ATAC-seq, single-cell multiome (ATAC and gene expression), and in situ technology. </p>
Collection Overview
Cellular identity, environment, stimuli, and physiological rhythms all require a static genome to respond dynamically, and sometimes reversibly while preserving the underlying genetic code. Epigenetic layers such as DNA methylation, and chromatin remodeling provide mechanisms for enabling these responses by altering accessibility and facilitating interactions between loci and with associated RNA and proteins. Although the stable maintenance of some epigenetic layers is essential, epigenetic regulation exhibits considerable plasticity, permitting the adaptability of a single genome into a functional organism.
Epigenetic dysregulation is implicated in a wide array of conditions and may occur in combination with genetic mutations or environmental insults. Understanding how these modifications to the DNA and chromatin alter their function and developing tools and therapies to restore function are of critical importance and are highly studied in many contexts of human health.
The growing toolkit of methods available in the field has allowed researchers to study the epigenome at several levels including detection (e.g., whole-genome bisulfite sequencing, chromatin immunoprecipitation, chromosome conformation capture, ATAC-seq), visualization (e.g., in situ microscopy), and editing (e.g., CRISPR). This methods collection aims to highlight such techniques and more, which enable the examination of both targeted and genome-wide epigenetic modifications at the DNA and chromatin levels.
Articles
Abstracts
Spatially resolved, integrated single-cell multiomic profiling of the transcriptome and epigenomic targets in frozen tissue sections
Ting Zhang1,
Saba Farassati1,
Alejandro Stark Quiroz1,
Yuanhang Liu2,
Tamas Ordog*3,
Jeong-Heon Lee*4
1Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota,
2Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota,
3Enteric NeuroScience Program and Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota; Gastroenterology Research Unit, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota,
4Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota; Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Gastroenterology Research Unit, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
Promoter interactome characterization in rare cell populations using low input catpure Hi-C (liCHi-C)
Llorenc Rovirosa1,
Laureano Tomas Daza2,
Alfonso Valencia3,
Biola M Javierre*4
1Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Spain,
21. Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Spain // 2. Barcelona Supercomputing Center, Barcelona, Barcelona, Spain ,
31. Barcelona Supercomputing Center, Barcelona, Barcelona, Spain // 2. Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain,
4Josep Carreras Leukaemia Research Institute and Institute for Health Science Research Germans Trias i Pujol, Badalona, Barcelona, Spain
Rapid quantification of global histone post translational modifications via intranuclear flow cytometry
Morgan Towriss*1,
Annie Ciernia*1
1Vancouver, BC, Canada
A flexible quantification pipeline of immunofluorescence assays to characterize various nuclear bodies and proteins in human T cells.
Valeria Di Gioia1
1Istituto Nazionale Genetica Molecolare