A KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy

Hematopoiesis is orchestrated by a succession of lineage- and stage-specific transcription factors working in concert with chromatin modifiers. Here, we explored the role of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor KAP1 in this process. The hematopoietic-restricted deletion of Kap1 in the mouse resulted in severe hypoproliferative anemia, with Kap1-deleted erythroblasts failing to induce mitophagy-associated genes, hence to eliminate mitochondria. This was due to persistent expression of microRNAs targeting mitophagy transcripts, itself secondary to a lack of repression by stage-specific KRAB-ZFPs. This KRAB/ KAP1-microRNA regulatory cascade is evolutionary conserved, as it also controls mitophagy during human erythropoiesis. A multilayered transcription regulatory system is thus unveiled, where protein- and RNA-based repressors are super-imposed in combinatorial fashion to govern the timely triggering of an essential differentiation event. Erythropoiesis releases about one hundred billion new red cells every day from the human adult bone marrow. This process is initiated by the differentiation of hematopoietic stem cells (HSC) into the earliest erythroid progenitor identified ex vivo, the slowly growing burst-forming unit-erythroid (BFU-E). This cell morphs into the rapidly dividing CFU-E (colony-forming

[1]  Helen M. Rowe,et al.  TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells , 2013, Genome research.

[2]  James H. Thomas,et al.  KAP1 regulates gene networks controlling T‐cell development and responsiveness , 2012, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[3]  D. Trono,et al.  The KRAB-ZFP/KAP1 system contributes to the early embryonic establishment of site-specific DNA methylation patterns maintained during development. , 2012, Cell reports.

[4]  D. Trono,et al.  Liver‐specific ablation of Krüppel‐associated box–associated protein 1 in mice leads to male‐predominant hepatosteatosis and development of liver adenoma , 2012, Hepatology.

[5]  Luca Pinello,et al.  Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. , 2012, Developmental cell.

[6]  T. Honjo,et al.  TRIM28 prevents autoinflammatory T cell development in vivo , 2012, Nature Immunology.

[7]  James H. Thomas,et al.  KAP1 regulates gene networks controlling mouse B-lymphoid cell differentiation and function. , 2012, Blood.

[8]  Ray M. Marín,et al.  Optimal Use of Conservation and Accessibility Filters in MicroRNA Target Prediction , 2012, PloS one.

[9]  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.

[10]  E. Laurenti,et al.  Lineage- and stage-restricted lentiviral vectors for the gene therapy of chronic granulomatous disease , 2011, Gene Therapy.

[11]  Jacques Rougemont,et al.  GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR , 2011, Database J. Biol. Databases Curation.

[12]  F. Bushman,et al.  A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing , 2011, BMC Genomics.

[13]  Jirí Vanícek,et al.  Efficient use of accessibility in microRNA target prediction , 2010, Nucleic Acids Res..

[14]  Helen M. Rowe,et al.  KAP1 controls endogenous retroviruses in embryonic stem cells , 2010, Nature.

[15]  C. Lawrie microRNA expression in erythropoiesis and erythroid disorders , 2009, British journal of haematology.

[16]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[17]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[18]  C. Sandi,et al.  KAP1-Mediated Epigenetic Repression in the Forebrain Modulates Behavioral Vulnerability to Stress , 2008, Neuron.

[19]  P. Leder,et al.  A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. , 2008, Developmental cell.

[20]  A. Hattersley,et al.  Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57 , 2008, Nature Genetics.

[21]  S. Goff,et al.  TRIM28 Mediates Primer Binding Site-Targeted Silencing of Murine Leukemia Virus in Embryonic Cells , 2007, Cell.

[22]  Y. Shiloh,et al.  Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway , 2006, Nature Cell Biology.

[23]  G. Maul,et al.  SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. , 2002, Genes & development.

[24]  Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[25]  Shankar Srinivas,et al.  Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus , 2001, BMC Developmental Biology.

[26]  J. Friedman,et al.  Targeting histone deacetylase complexes via KRAB-zinc finger proteins: the PHD and bromodomains of KAP-1 form a cooperative unit that recruits a novel isoform of the Mi-2alpha subunit of NuRD. , 2001, Genes & development.

[27]  P. L. Chen,et al.  Sequence-specific transcriptional corepressor function for BRCA1 through a novel zinc finger protein, ZBRK1. , 2000, Molecular cell.

[28]  P. Chambon,et al.  Mice lacking the transcriptional corepressor TIF1beta are defective in early postimplantation development. , 2000, Development.

[29]  R. Losson,et al.  Interaction with members of the heterochromatin protein 1 (HP1) family and histone deacetylation are differentially involved in transcriptional silencing by members of the TIF1 family , 1999, The EMBO journal.

[30]  M Aguet,et al.  Inducible gene targeting in mice , 1995, Science.

[31]  J. Martial,et al.  The evolutionarily conserved Krüppel-associated box domain defines a subfamily of eukaryotic multifingered proteins. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[32]  D. Mccormick Sequence the Human Genome , 1986, Bio/Technology.

[33]  T. Papayannopoulou,et al.  HEL cells: a new human erythroleukemia cell line with spontaneous and induced globin expression. , 1982, Science.