An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype

[1]  B. van Steensel,et al.  CTCF and cohesin promote focal detachment of DNA from the nuclear lamina , 2022, Genome Biology.

[2]  P. Park,et al.  The 4D Nucleome Data Portal: a resource for searching and visualizing curated nucleomics data , 2021, bioRxiv.

[3]  B. van Steensel,et al.  CTCF and cohesin promote focal detachment of DNA from the nuclear lamina , 2021, bioRxiv.

[4]  B. van Steensel,et al.  Rapid depletion of CTCF and cohesin proteins reveals dynamic features of chromosome architecture , 2021, bioRxiv.

[5]  Ryan L. Collins,et al.  Genome-wide enhancer maps link risk variants to disease genes , 2021, Nature.

[6]  D. Rader,et al.  Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. , 2021, Cell stem cell.

[7]  Michael L. Waskom,et al.  Seaborn: Statistical Data Visualization , 2021, J. Open Source Softw..

[8]  Martin J. Aryee,et al.  Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer , 2020, Cell.

[9]  Michael J. Purcaro,et al.  Expanded encyclopaedias of DNA elements in the human and mouse genomes , 2020, Nature.

[10]  M. Porteus,et al.  Improving the safety of human pluripotent stem cell therapies using genome-edited orthogonal safeguards , 2020, Nature Communications.

[11]  Jason Brunson,et al.  ggalluvial: Layered Grammar for Alluvial Plots , 2020, J. Open Source Softw..

[12]  N. Briand,et al.  Lamina-associated domains: peripheral matters and internal affairs , 2020, Genome Biology.

[13]  D. Gilbert,et al.  SPIN reveals genome-wide landscape of nuclear compartmentalization , 2020, Genome Biology.

[14]  V. Nizet,et al.  Upon microbial challenge, human neutrophils undergo rapid changes in nuclear architecture and chromatin folding to orchestrate an immediate inflammatory gene program , 2020, Genes & development.

[15]  Kohske Takahashi,et al.  Welcome to the Tidyverse , 2019, J. Open Source Softw..

[16]  R. Irizarry.  ggplot2 , 2019, Introduction to Data Science.

[17]  Wei Xie,et al.  The role of 3D genome organization in development and cell differentiation , 2019, Nature Reviews Molecular Cell Biology.

[18]  Elie N. Farah,et al.  Transcriptionally Active HERV-H Retrotransposons Demarcate Topologically Associating Domains in Human Pluripotent Stem Cells , 2019, Nature Genetics.

[19]  Howard Y. Chang,et al.  Activation of PDGF Pathway Links LMNA Mutation to Dilated Cardiomyopathy , 2019, Nature.

[20]  M. Cosma,et al.  Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo , 2019, Nucleic acids research.

[21]  P. Sivaramakrishnan,et al.  H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis , 2019, bioRxiv.

[22]  K. Loh,et al.  Efficient Differentiation of Human Pluripotent Stem Cells into Liver Cells. , 2019, Journal of visualized experiments : JoVE.

[23]  L. Mirny,et al.  Heterochromatin drives compartmentalization of inverted and conventional nuclei , 2019, Nature.

[24]  M. Torres-Padilla,et al.  Genome-lamina interactions are established de novo in the early mouse embryo , 2019, Nature.

[25]  S. Lomvardas,et al.  Olfactory receptor genes make the case for inter-chromosomal interactions. , 2019, Current opinion in genetics & development.

[26]  Gabriel N. Aughey,et al.  DamID as a versatile tool for understanding gene regulation , 2019, Development.

[27]  Nezar Abdennur,et al.  Cooler: scalable storage for Hi-C data and other genomically-labeled arrays , 2019, bioRxiv.

[28]  J. Epstein,et al.  Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9me2 domains , 2019, Development.

[29]  Siddharth S. Dey,et al.  scDam&T‐seq combines DNA adenine methyltransferase-based labeling of protein-DNA contact sites with transcriptome sequencing to analyze regulatory programs in single cells , 2019, Nature Biotechnology.

[30]  V. Corces,et al.  Organizational principles of 3D genome architecture , 2018, Nature Reviews Genetics.

[31]  William Stafford Noble,et al.  Integrative detection and analysis of structural variation in cancer genomes , 2018, Nature Genetics.

[32]  James Taylor,et al.  Lamins organize the global three-dimensional genome from the nuclear periphery , 2017, bioRxiv.

[33]  Jonas Paulsen,et al.  The lipodystrophic hotspot lamin A p.R482W mutation deregulates the mesodermal inducer T/Brachyury and early vascular differentiation gene networks , 2018, Human molecular genetics.

[34]  I. Weissman,et al.  A Roadmap for Human Liver Differentiation from Pluripotent Stem Cells , 2018, Cell reports.

[35]  Manolis Kellis,et al.  Chromatin-state discovery and genome annotation with ChromHMM , 2017, Nature Protocols.

[36]  Jacob Schreiber,et al.  Pomegranate: fast and flexible probabilistic modeling in python , 2017, J. Mach. Learn. Res..

[37]  J. Epstein,et al.  Genome-Nuclear Lamina Interactions Regulate Cardiac Stem Cell Lineage Restriction , 2017, Cell.

[38]  L. Studer,et al.  A Modular Platform for Differentiation of Human PSCs into All Major Ectodermal Lineages. , 2017, Cell stem cell.

[39]  M. Hetzer,et al.  Nucleolar expansion and elevated protein translation in premature aging , 2017, Nature Communications.

[40]  Howard Y. Chang,et al.  Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs , 2017, Circulation research.

[41]  Bas van Steensel,et al.  Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression , 2017, Cell.

[42]  E. C. Schirmer,et al.  Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments , 2016, bioRxiv.

[43]  A. Sharp,et al.  Foxa2 identifies a cardiac progenitor population with ventricular differentiation potential , 2017, Nature Communications.

[44]  Victor O. Leshyk,et al.  The 4D nucleome project , 2017, Nature.

[45]  Pang Wei Koh,et al.  An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development , 2016, Scientific Data.

[46]  Pang Wei Koh,et al.  Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types , 2016, Cell.

[47]  E. C. Schirmer,et al.  Tissue-Specific Gene Repositioning by Muscle Nuclear Membrane Proteins Enhances Repression of Critical Developmental Genes during Myogenesis , 2016, Molecular cell.

[48]  Lior Pachter,et al.  Differential analysis of RNA-seq incorporating quantification uncertainty , 2016, Nature Methods.

[49]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[50]  Li Wang,et al.  Perinuclear Anchoring of H3K9-Methylated Chromatin Stabilizes Induced Cell Fate in C. elegans Embryos , 2015, Cell.

[51]  Siddharth S. Dey,et al.  Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells , 2015, Cell.

[52]  Xiaobin Zheng,et al.  Identification of lamin B–regulated chromatin regions based on chromatin landscapes , 2015, Molecular biology of the cell.

[53]  Alice Barateau,et al.  The p.R482W substitution in A-type lamins deregulates SREBP1 activity in Dunnigan-type familial partial lipodystrophy. , 2015, Human molecular genetics.

[54]  M. Garcia-Parajo,et al.  Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo , 2015, Cell.

[55]  S. Wheelan,et al.  Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins , 2015, The Journal of cell biology.

[56]  Yanli Wang,et al.  Topologically associating domains are stable units of replication-timing regulation , 2014, Nature.

[57]  G. Fishman,et al.  Identification and Purification of Human Induced Pluripotent Stem Cell-Derived Atrial-Like Cardiomyocytes Based on Sarcolipin Expression , 2014, PloS one.

[58]  Fidel Ramírez,et al.  deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..

[59]  A. Oldenburg,et al.  Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations , 2014, Nucleic acids research.

[60]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[61]  I. Weissman,et al.  Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations. , 2014, Cell stem cell.

[62]  Kajia Cao,et al.  Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape , 2013, Genes & development.

[63]  P. A. Pérez-Mancera,et al.  Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence , 2013, Genes & development.

[64]  S. Anderson,et al.  Directed differentiation and functional maturation of cortical interneurons from human embryonic stem cells. , 2013, Cell stem cell.

[65]  W. Bickmore,et al.  Single-Cell Dynamics of Genome-Nuclear Lamina Interactions , 2013, Cell.

[66]  Guillaume J. Filion,et al.  A network model of the molecular organization of chromatin in Drosophila. , 2013, Molecular cell.

[67]  Manolis Kellis,et al.  Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence , 2013, Genome research.

[68]  L. Peichl,et al.  LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation , 2013, Cell.

[69]  Jean-Marie Rouillard,et al.  Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes , 2012, Proceedings of the National Academy of Sciences.

[70]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[71]  Kurt Hornik,et al.  The Comprehensive R Archive Network , 2012 .

[72]  Jun S. Song,et al.  Statistical Applications in Genetics and Molecular Biology Normalization , bias correction , and peak calling for ChIP-seq , 2012 .

[73]  Gordon Keller,et al.  SIRPA is a specific cell-surface marker for isolating cardiomyocytes derived from human pluripotent stem cells , 2011, Nature Biotechnology.

[74]  D. Surmeier,et al.  Floor plate-derived dopamine neurons from hESCs efficiently engraft in animal models of PD , 2016 .

[75]  Brent S. Pedersen,et al.  Pybedtools: a flexible Python library for manipulating genomic datasets and annotations , 2011, Bioinform..

[76]  Chee Seng Chan,et al.  CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells , 2011, Nature Genetics.

[77]  Gaël Varoquaux,et al.  The NumPy Array: A Structure for Efficient Numerical Computation , 2011, Computing in Science & Engineering.

[78]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[79]  Guillaume J. Filion,et al.  Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells , 2010, Cell.

[80]  P. Flicek,et al.  Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. , 2010, Molecular cell.

[81]  A. Ponti,et al.  The spatial dynamics of tissue-specific promoters during C. elegans development. , 2010, Genes & development.

[82]  D. Kavanagh,et al.  Cell-specific and lamin-dependent targeting of novel transmembrane proteins in the nuclear envelope , 2010, Cellular and Molecular Life Sciences.

[83]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[84]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[85]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[86]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[87]  K. Ocorr,et al.  Transcription factor neuromancer/TBX20 is required for cardiac function in Drosophila with implications for human heart disease , 2008, Proceedings of the National Academy of Sciences.

[88]  Bin Zhou,et al.  Epicardial progenitors contribute to the cardiomyocyte lineage in the developing heart , 2008, Nature.

[89]  L. Wessels,et al.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions , 2008, Nature.

[90]  Mauro W. Costa,et al.  Mutations in cardiac T-box factor gene TBX20 are associated with diverse cardiac pathologies, including defects of septation and valvulogenesis and cardiomyopathy. , 2007, American journal of human genetics.

[91]  H. Worman,et al.  "Laminopathies": a wide spectrum of human diseases. , 2007, Experimental cell research.

[92]  Bas van Steensel,et al.  Detection of in vivo protein–DNA interactions using DamID in mammalian cells , 2007, Nature Protocols.

[93]  S. Grewal,et al.  Transcription and RNA interference in the formation of heterochromatin , 2007, Nature.

[94]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[95]  C. Stewart,et al.  The laminopathies: the functional architecture of the nucleus and its contribution to disease. , 2006, Annual review of genomics and human genetics.

[96]  S. Henikoff,et al.  Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase , 2000, Nature Biotechnology.

[97]  G. Gogstad,et al.  Characterization of the proteins of isolated human platelet alpha-granules. Evidence for a separate alpha-granule-pool of the glycoproteins IIb and IIIa. , 1981, Biochimica et biophysica acta.

[98]  H. Akaike.  A new look at the statistical model identification , 1974 .

[99]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[100]  Melissa C. Greven,et al.  An integrated encyclopedia of DNA elements in the human genome , 2014 .

[101]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[102]  I. Amit,et al.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome. , 2009, Science.