Primate-specific transposable elements shape transcriptional networks during human development

[1]  D. Trono,et al.  Statistical learning quantifies transposable element-mediated cis-regulation , 2022, bioRxiv.

[2]  J. Wysocka,et al.  Roles of transposable elements in the regulation of mammalian transcription , 2022, Nature Reviews Molecular Cell Biology.

[3]  A. Scialdone,et al.  Single-cell transcriptomic characterization of a gastrulating human embryo , 2021, Nature.

[4]  L. Muglia,et al.  Endogenous retroviruses drive lineage-specific regulatory evolution across primate and rodent placentae. , 2021, Molecular biology and evolution.

[5]  S. Behjati,et al.  A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre , 2021, Nature Communications.

[6]  M. Smidt,et al.  ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters , 2021, Genome research.

[7]  A. Hutchins,et al.  Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE , 2021, Nature Communications.

[8]  D. Trono,et al.  Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain , 2020, bioRxiv.

[9]  Andrew J. Hill,et al.  A human cell atlas of fetal chromatin accessibility , 2020, Science.

[10]  A. Scialdone,et al.  A spatially resolved single cell atlas of human gastrulation , 2020, bioRxiv.

[11]  A. van Oudenaarden,et al.  An in vitro model of early anteroposterior organization during human development , 2020, Nature.

[12]  A. Sharov,et al.  Generation and Profiling of 2,135 Human ESC Lines for the Systematic Analyses of Cell States Perturbed by Inducing Single Transcription Factors. , 2020, Cell reports.

[13]  G. Kristiansen,et al.  Unique and redundant roles of SOX2 and SOX17 in regulating the germ cell tumor fate , 2020, International journal of cancer.

[14]  J. Wysocka,et al.  Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes , 2020, Philosophical Transactions of the Royal Society B.

[15]  Erica C. Pehrsson,et al.  The epigenomic landscape of transposable elements across normal human development and anatomy , 2019, Nature Communications.

[16]  Manolis Kellis,et al.  Human Primordial Germ Cells Are Specified from Lineage-Primed Progenitors , 2019, Cell reports.

[17]  B. Deplancke,et al.  Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons , 2019, Science Advances.

[18]  D. Bourc’his,et al.  The diverse roles of DNA methylation in mammalian development and disease , 2019, Nature Reviews Molecular Cell Biology.

[19]  Christina S. Leslie,et al.  FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation , 2019, Cell reports.

[20]  Paul J. Hoffman,et al.  Comprehensive Integration of Single-Cell Data , 2018, Cell.

[21]  R. Jaenisch,et al.  Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs , 2019, Cell stem cell.

[22]  Howard Y. Chang,et al.  Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion , 2019, Nature Biotechnology.

[23]  J. Marioni,et al.  A single-cell molecular map of mouse gastrulation and early organogenesis , 2019, Nature.

[24]  Huanming Yang,et al.  An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos , 2019, Nature Communications.

[25]  Jun Sese,et al.  ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data , 2018, EMBO reports.

[26]  T. Swigut,et al.  Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation , 2018, eLife.

[27]  Xuepeng Wang,et al.  Chromatin analysis in human early development reveals epigenetic transition during ZGA , 2018, Nature.

[28]  Lei Gao,et al.  Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution , 2018, Cell.

[29]  William A. Pastor,et al.  TFAP2C regulates transcription in human naive pluripotency by opening enhancers , 2018, Nature Cell Biology.

[30]  Ting Wang,et al.  Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re‐Visiting the “Gene‐Battery” Model , 2018, BioEssays : news and reviews in molecular, cellular and developmental biology.

[31]  Yixuan Wang,et al.  The Role of KRAB-ZFPs in Transposable Element Repression and Mammalian Evolution. , 2017, Trends in genetics : TIG.

[32]  Christopher D. Brown,et al.  Transposable elements are the primary source of novelty in primate gene regulation , 2017, Genome research.

[33]  D. Trono,et al.  KRAB zinc finger proteins , 2017, Development.

[34]  André F. Rendeiro,et al.  Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells , 2017, bioRxiv.

[35]  I. Inoue,et al.  Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses , 2017, PLoS Genetics.

[36]  S. Hainsworth,et al.  A CRITICAL ASSESSMENT , 2014 .

[37]  D. Trono,et al.  KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks , 2017, Nature.

[38]  C. Feschotte,et al.  Regulatory activities of transposable elements: from conflicts to benefits , 2016, Nature Reviews Genetics.

[39]  J. Joly,et al.  Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR , 2016, Genome Biology.

[40]  Helen M. Rowe,et al.  Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues. , 2016, Developmental cell.

[41]  C. Feschotte,et al.  Regulatory evolution of innate immunity through co-option of endogenous retroviruses , 2016, Science.

[42]  D. Trono,et al.  The developmental control of transposable elements and the evolution of higher species. , 2015, Annual review of cell and developmental biology.

[43]  M. Azim Surani,et al.  A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development , 2015, Cell.

[44]  M. Pavlicev,et al.  Detecting Endogenous Retrovirus-Driven Tissue-Specific Gene Transcription , 2015, Genome biology and evolution.

[45]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[46]  E. Füchtbauer,et al.  The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses , 2015, Genes & development.

[47]  Howard Y. Chang,et al.  Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells , 2015, Nature.

[48]  H. Ng,et al.  Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells. , 2015, Cell stem cell.

[49]  Zhihai Ma,et al.  Widespread contribution of transposable elements to the innovation of gene regulatory networks , 2014, Genome research.

[50]  L. Hurst,et al.  Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells , 2014, Nature.

[51]  David Haussler,et al.  An evolutionary arms race between KRAB zinc finger genes 91/93 and SVA/L1 retrotransposons , 2014, Nature.

[52]  S. Yamanaka,et al.  Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential , 2014, Proceedings of the National Academy of Sciences.

[53]  F. Tang,et al.  The DNA methylation landscape of human early embryos , 2014, Nature.

[54]  Aviv Regev,et al.  DNA methylation dynamics of the human preimplantation embryo , 2014, Nature.

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

[56]  Piotr J. Balwierz,et al.  ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs , 2014, Genome research.

[57]  A. Sandelin,et al.  Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance , 2014, Nature Genetics.

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

[59]  Charity W. Law,et al.  voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.

[60]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[61]  G. Bourque,et al.  The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements , 2013, PLoS genetics.

[62]  Jeremy Luban,et al.  HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency , 2012, Retrovirology.

[63]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[64]  G. Bourque,et al.  Transposable elements have rewired the core regulatory network of human embryonic stem cells , 2010, Nature Genetics.

[65]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[66]  D. Mager,et al.  Endogenous retroviral LTRs as promoters for human genes: a critical assessment. , 2009, Gene.

[67]  E. Liu,et al.  Evolution of the mammalian transcription factor binding repertoire via transposable elements. , 2008, Genome research.

[68]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[69]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[70]  W. Lim,et al.  Complex inheritance of familial hypercholanemia with associated mutations in TJP2 and BAAT , 2003, Nature Genetics.

[71]  R. Britten,et al.  Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty , 1971, The Quarterly Review of Biology.

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

[73]  D. Duboule.  Temporal colinearity and the phylotypic progression: a basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony. , 1994, Development (Cambridge, England). Supplement.