Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia.

[1]  Janet M. Young,et al.  Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila , 2020, bioRxiv.

[2]  Michael Q. Zhang,et al.  Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9 , 2020, Genome Biology.

[3]  S. Mirarab,et al.  Sequence Analysis , 2020, Encyclopedia of Bioinformatics and Computational Biology.

[4]  G. Faulkner,et al.  Overcoming challenges and dogmas to understand the functions of pseudogenes , 2019, Nature Reviews Genetics.

[5]  B. Eliceiri,et al.  Uniquely human CHRFAM7A gene increases the hematopoietic stem cell reservoir in mice and amplifies their inflammatory response , 2019, Proceedings of the National Academy of Sciences.

[6]  Zhiqiang Gao,et al.  GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes , 2019, Genome research.

[7]  David Haussler,et al.  The UCSC Genome Browser database: 2019 update , 2018, Nucleic Acids Res..

[8]  A. Dean,et al.  Fetal γ-globin genes are regulated by the BGLT3 long noncoding RNA locus. , 2018, Blood.

[9]  L. Patrushev,et al.  Pseudogenes as Functionally Significant Elements of the Genome , 2018, Biochemistry (Moscow).

[10]  J. D. Engel,et al.  Long non-coding RNA-dependent mechanism to regulate heme biosynthesis and erythrocyte development , 2018, Nature Communications.

[11]  A. McLysaght,et al.  Pseudogenes Provide Evolutionary Evidence for the Competitive Endogenous RNA Hypothesis , 2018, Molecular biology and evolution.

[12]  Alex A. Pollen,et al.  Transcriptional fates of human-specific segmental duplications in brain , 2018, Genome research.

[13]  S. Cichon,et al.  Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus , 2017, Nature Communications.

[14]  Michael Q. Zhang,et al.  In Situ Capture of Chromatin Interactions by Biotinylated dCas9 , 2017, Cell.

[15]  R. Hardison,et al.  Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element , 2017, Genes & development.

[16]  Sudhir Kumar,et al.  TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. , 2017, Molecular biology and evolution.

[17]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[18]  E. Eichler,et al.  Human adaptation and evolution by segmental duplication. , 2016, Current opinion in genetics & development.

[19]  M. Long,et al.  LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans , 2016, Genome research.

[20]  J. F. Storz Gene Duplication and Evolutionary Innovations in Hemoglobin-Oxygen Transport. , 2016, Physiology.

[21]  J. Scheller,et al.  A widespread sequence-specific mRNA decay pathway mediated by hnRNPs A1 and A2/B1 , 2016, Genes & development.

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

[23]  Jacob C. Ulirsch,et al.  Advances in understanding erythropoiesis: evolving perspectives , 2016, British journal of haematology.

[24]  Gene W. Yeo,et al.  Robust transcriptome-wide discovery of RNA binding protein binding sites with enhanced CLIP (eCLIP) , 2016, Nature Methods.

[25]  Jianzhi Zhang,et al.  Are Human Translated Pseudogenes Functional? , 2016, Molecular biology and evolution.

[26]  Guo-Dong Wang,et al.  Out of southern East Asia: the natural history of domestic dogs across the world , 2015, Cell Research.

[27]  Pak Chung Sham,et al.  GWASdb v2: an update database for human genetic variants identified by genome-wide association studies , 2015, Nucleic Acids Res..

[28]  P. Pandolfi,et al.  Pseudogenes in Human Cancer , 2015, Front. Med..

[29]  Alfonso Valencia,et al.  APPRIS WebServer and WebServices , 2015, Nucleic Acids Res..

[30]  Laura J. Norton,et al.  Editing the genome to introduce a beneficial naturally occurring mutation associated with increased fetal globin , 2015, Nature Communications.

[31]  Jun S. Liu,et al.  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.

[32]  Thomas M. Keane,et al.  The BRAF Pseudogene Functions as a Competitive Endogenous RNA and Induces Lymphoma In Vivo , 2015, Cell.

[33]  M. Long,et al.  New genes contribute to genetic and phenotypic novelties in human evolution. , 2014, Current opinion in genetics & development.

[34]  Haiwang Yang,et al.  Expression Profile and Gene Age Jointly Shaped the Genome-Wide Distribution of Premature Termination Codons in a Drosophila melanogaster Population , 2014, Molecular biology and evolution.

[35]  J. D. Engel,et al.  Developmental transcriptome analysis of human erythropoiesis. , 2014, Human molecular genetics.

[36]  Gary D Bader,et al.  A draft map of the human proteome , 2014, Nature.

[37]  D. Zheng,et al.  Characterization of Human Pseudogene-Derived Non-Coding RNAs for Functional Potential , 2014, PloS one.

[38]  Zhaolei Zhang,et al.  Pseudogene Evolution in the Human Genome , 2014 .

[39]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[40]  Hui Zhou,et al.  starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data , 2013, Nucleic Acids Res..

[41]  Traver Hart,et al.  Finding the active genes in deep RNA-seq gene expression studies , 2013, BMC Genomics.

[42]  M. Long,et al.  New genes as drivers of phenotypic evolution , 2013, Nature Reviews Genetics.

[43]  Hongen Zhang,et al.  RCircos: an R package for Circos 2D track plots , 2013, BMC Bioinformatics.

[44]  A. D. L. de la Cruz,et al.  Stepwise Evolution of Essential Centromere Function in a Drosophila Neogene , 2013, Science.

[45]  Xiu-Jie Wang,et al.  Pseudogenes: pseudo or real functional elements? , 2013, Journal of genetics and genomics = Yi chuan xue bao.

[46]  Li Ding,et al.  Retrotransposition of gene transcripts leads to structural variation in mammalian genomes , 2013, Genome Biology.

[47]  Osamu Tanabe,et al.  Lysine-specific demethylase 1 is a therapeutic target for fetal hemoglobin induction , 2013, Nature Medicine.

[48]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[49]  R. Hardison Evolution of hemoglobin and its genes. , 2012, Cold Spring Harbor perspectives in medicine.

[50]  J. Sikela,et al.  Evolution of genetic and genomic features unique to the human lineage , 2012, Nature Reviews Genetics.

[51]  L. Poliseno Pseudogenes: Newly Discovered Players in Human Cancer , 2012, Science Signaling.

[52]  R. Guigó,et al.  Modelling and simulating generic RNA-Seq experiments with the flux simulator , 2012, Nucleic acids research.

[53]  M. Gerstein,et al.  The GENCODE pseudogene resource , 2012, Genome Biology.

[54]  Wei Li,et al.  RSeQC: quality control of RNA-seq experiments , 2012, Bioinform..

[55]  Ramón Doallo,et al.  CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.

[56]  Yukio Nakamura,et al.  Establishment of Immortalized Human Erythroid Progenitor Cell Lines Able to Produce Enucleated Red Blood Cells , 2012, PloS one.

[57]  S. Dhanasekaran,et al.  Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers , 2012, Cell.

[58]  G. Patrinos,et al.  A Single Nucleotide Polymorphism in the HBBP1 Gene in the Human β-Globin Locus is Associated with a Mild β-Thalassemia Disease Phenotype , 2012, Hemoglobin.

[59]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[60]  Harvey F Lodish,et al.  From stem cell to red cell: regulation of erythropoiesis at multiple levels by multiple proteins, RNAs, and chromatin modifications. , 2011, Blood.

[61]  Cong Peng,et al.  Correction of Sickle Cell Disease in Adult Mice by Interference with Fetal Hemoglobin Silencing , 2011, Science.

[62]  Gautier Koscielny,et al.  Ensembl 2012 , 2011, Nucleic Acids Res..

[63]  J. Kleinman,et al.  Spatiotemporal transcriptome of the human brain , 2011, Nature.

[64]  M. Long,et al.  Accelerated Recruitment of New Brain Development Genes into the Human Genome , 2011, PLoS biology.

[65]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[66]  Peng Ji,et al.  Formation of mammalian erythrocytes: chromatin condensation and enucleation. , 2011, Trends in cell biology.

[67]  Manyuan Long,et al.  New Genes in Drosophila Quickly Become Essential , 2010, Science.

[68]  Jianzhi Zhang,et al.  Pseudogenes and Their Evolution , 2010 .

[69]  Henrik Kaessmann,et al.  Origins, evolution, and phenotypic impact of new genes. , 2010, Genome research.

[70]  S. Liebhaber,et al.  Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes. , 2010, Nature communications.

[71]  P. Pandolfi,et al.  A coding-independent function of gene and pseudogene mRNAs regulates tumour biology , 2010, Nature.

[72]  M. Long,et al.  Tight Junction–associated MARVEL Proteins MarvelD3, Tricellulin, and Occludin Have Distinct but Overlapping Functions , 2010, Molecular biology of the cell.

[73]  F. Kondrashov,et al.  The evolution of gene duplications: classifying and distinguishing between models , 2010, Nature Reviews Genetics.

[74]  G. Reid,et al.  A rapid and sensitive method to detect siRNA-mediated mRNA cleavage in vivo using 5′ RACE and a molecular beacon probe , 2009, Nucleic acids research.

[75]  David Haussler,et al.  The UCSC Genome Browser database: update 2010 , 2009, Nucleic Acids Res..

[76]  Wanling Yang,et al.  Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference , 2009, BMC Bioinformatics.

[77]  J. Côté,et al.  hnRNP A1 regulates UV-induced NF-κB signalling through destabilization of cIAP1 mRNA , 2009, Cell Death and Differentiation.

[78]  F. Hoffmann,et al.  Differential loss of embryonic globin genes during the radiation of placental mammals , 2008, Proceedings of the National Academy of Sciences.

[79]  C. Lowrey,et al.  A cell stress signaling model of fetal hemoglobin induction: what doesn't kill red blood cells may make them stronger. , 2008, Experimental hematology.

[80]  Kazutaka Katoh,et al.  Recent developments in the MAFFT multiple sequence alignment program , 2008, Briefings Bioinform..

[81]  Oliver H. Tam,et al.  Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes , 2008, Nature.

[82]  Geoffrey J Faulkner,et al.  A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. , 2008, Genomics.

[83]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[84]  G. Keller,et al.  Development of the hemangioblast defines the onset of hematopoiesis in human ES cell differentiation cultures. , 2007, Blood.

[85]  M. Long Faculty Opinions recommendation of The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. , 2006 .

[86]  Koji Kadota,et al.  ROKU: a novel method for identification of tissue-specific genes , 2006, BMC Bioinformatics.

[87]  Jianzhi Zhang Evolution by gene duplication: an update , 2003 .

[88]  Phillip A Sharp,et al.  Predictive Identification of Exonic Splicing Enhancers in Human Genes , 2002, Science.

[89]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[90]  F. Alt,et al.  The T Cell Leukemia Oncoprotein SCL/tal-1 Is Essential for Development of All Hematopoietic Lineages , 1996, Cell.

[91]  C. Begley,et al.  Absence of yolk sac hematopoiesis from mice with a targeted disruption of the scl gene. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[92]  Peilin Xu,et al.  Primate η-globin DNA sequences and man's place among the great apes , 1986, Nature.

[93]  S. Orkin,et al.  Hydroxyurea enhances fetal hemoglobin production in sickle cell anemia. , 1984, The Journal of clinical investigation.

[94]  G. Brownlee,et al.  A pseudogene structure in 5S DNA of Xenopus laevis , 1977, Cell.

[95]  Yusuke Nakamura,et al.  A genome-wide association identified the common genetic variants influence disease severity in β0-thalassemia/hemoglobin E , 2009, Human Genetics.

[96]  N. Vinckenbosch,et al.  RNA-based gene duplication: mechanistic and evolutionary insights , 2009, Nature Reviews Genetics.

[97]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[98]  K. Nicholas,et al.  GeneDoc: Analysis and visualization of genetic variation , 1997 .

[99]  J. Hirschhorn,et al.  Supporting Online Material Materials and Methods Figs. S1 to S10 Tables S1 to S7 References Human Fetal Hemoglobin Expression Is Regulated by the Developmental Stage-specific Repressor Bcl11a , 2022 .