Baf45a Mediated Chromatin Remodeling Promotes Transcriptional Activation for Osteogenesis and Odontogenesis

Chromatin remodeling, specifically the tissue-specific regulation in mineralized tissues, is an understudied avenue of gene regulation. Here we show that Baf45a and Baf45d, two Baf45 homologs belong to ATPase-dependent SWI/SNF chromatin remodeling complex, preferentially expressed in osteoblasts and odontoblasts compared to Baf45b and Baf45c. Recently, biochemical studies revealed that BAF45A associates with Polybromo-associated BAF (PBAF) complex. However, the BAF45D subunit belongs to the polymorphic canonical BRG1-associated factor (cBAF) complex. Protein profiles of osteoblast and odontoblast differentiation uncovered a significant increase of BAF45A and PBAF subunits during early osteoblast and odontoblast maturation. Chromatin immunoprecipitation sequencing (ChIP-seq) during the bone marrow stromal cells (BMSCs) differentiation showed higher histone H3K9 and H3K27 acetylation modifications in the promoter of Baf45a and Baf45d and increased binding of bone and tooth specific transcription factor RUNX2. Overexpression of Baf45a in osteoblasts activates genes essential for the progression of osteoblast maturation and mineralization. Furthermore, shRNA-mediated knockdown of Baf45a in odontoblasts leads to markedly altered genes responsible for the proliferation, apoptosis, DNA repair, and modest decrease in dentinogenic marker gene expression. Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) assay in Baf45a knockout osteoblasts revealed a noticeable reduction in chromatin accessibility of osteoblast and odontoblast specific genes, along with transcription factor Atf4 and Klf4. Craniofacial mesenchyme-specific loss of Baf45a modestly reduced the mineralization of the tooth and mandibular bone. These findings indicated that BAF45A-dependent mineralized tissue-specific chromatin remodeling through PBAF-RUNX2 crosstalk results in transcriptional activation is critical for early differentiation and matrix maturation of mineralized tissues.

[1]  S. Georgieva,et al.  The DPF Domain As a Unique Structural Unit Participating in Transcriptional Activation, Cell Differentiation, and Malignant Transformation , 2020, Acta naturae.

[2]  M. Longaker,et al.  Mechanisms of bone development and repair , 2020, Nature Reviews Molecular Cell Biology.

[3]  A. Sengupta,et al.  Pbrm1 Steers Mesenchymal Stromal Cell Osteolineage Differentiation by Integrating PBAF-Dependent Chromatin Remodeling and BMP/TGF-β Signaling. , 2020, Cell reports.

[4]  S. Georgieva,et al.  PBAF lacking PHD domains maintains transcription in human neutrophils. , 2019, Biochimica et biophysica acta. Molecular cell research.

[5]  K. Kerl,et al.  The BAF complex in development and disease , 2019, Epigenetics & Chromatin.

[6]  Anders K. Haakonsson,et al.  Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis , 2019, Nature Genetics.

[7]  M. Rehan,et al.  MICROmanagement of Runx2 Function in Skeletal Cells , 2019, Current Molecular Biology Reports.

[8]  Jesse R. Dixon,et al.  A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells , 2018, Nature Communications.

[9]  J. Ranish,et al.  Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes , 2018, Cell.

[10]  G. Almouzni,et al.  Chromatin plasticity: A versatile landscape that underlies cell fate and identity , 2018, Science.

[11]  C. Lengner,et al.  The microRNA-23a cluster regulates the developmental HoxA cluster function during osteoblast differentiation , 2018, The Journal of Biological Chemistry.

[12]  C. Yoshida,et al.  Runx2 is required for the proliferation of osteoblast progenitors and induces proliferation by regulating Fgfr2 and Fgfr3 , 2018, Scientific Reports.

[13]  C. Lengner,et al.  Epigenetic remodeling and modification to preserve skeletogenesis in vivo , 2018, Connective tissue research.

[14]  Nhuong V. Nguyen,et al.  Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry , 2018, Nature Communications.

[15]  Tran Tuoc,et al.  Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders , 2017, Front. Mol. Neurosci..

[16]  Yu. P. Simonov,et al.  Stability of the PHF10 subunit of PBAF signature module is regulated by phosphorylation: role of β-TrCP , 2017, Scientific Reports.

[17]  Changchun Zhou,et al.  Epigenetics in Odontogenesis and its Influences. , 2017, Current stem cell research & therapy.

[18]  Janet Iwasa,et al.  Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes , 2017, Nature Reviews Molecular Cell Biology.

[19]  G. Stein,et al.  Chromatin dynamics regulate mesenchymal stem cell lineage specification and differentiation to osteogenesis. , 2017, Biochimica et biophysica acta. Gene regulatory mechanisms.

[20]  G. Crabtree,et al.  The BAF45a/PHF10 subunit of SWI/SNF-like chromatin remodeling complexes is essential for hematopoietic stem cell maintenance. , 2017, Experimental hematology.

[21]  J. Millán,et al.  Conditional Alpl Ablation Phenocopies Dental Defects of Hypophosphatasia , 2017, Journal of dental research.

[22]  J. Staiger,et al.  mSWI/SNF (BAF) Complexes Are Indispensable for the Neurogenesis and Development of Embryonic Olfactory Epithelium , 2016, PLoS genetics.

[23]  G. Crabtree,et al.  The Many Roles of BAF (mSWI/SNF) and PBAF Complexes in Cancer. , 2016, Cold Spring Harbor perspectives in medicine.

[24]  E. Moran,et al.  Glucocorticoid receptor-mediated cis-repression of osteogenic genes requires BRM-SWI/SNF☆ , 2016, Bone reports.

[25]  G. Stein,et al.  Non-coding RNAs: Epigenetic regulators of bone development and homeostasis. , 2015, Bone.

[26]  G. Stein,et al.  Multiple levels of epigenetic control for bone biology and pathology. , 2015, Bone.

[27]  A. V. van Wijnen,et al.  Chromatin modifiers and histone modifications in bone formation, regeneration, and therapeutic intervention for bone-related disease. , 2015, Bone.

[28]  J. Pike,et al.  Epigenetic histone modifications and master regulators as determinants of context dependent nuclear receptor activity in bone cells. , 2015, Bone.

[29]  J. C. Clarke,et al.  MicroRNA 665 Regulates Dentinogenesis through MicroRNA-Mediated Silencing and Epigenetic Mechanisms , 2015, Molecular and Cellular Biology.

[30]  G. Crabtree,et al.  Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics , 2015, Science Advances.

[31]  Howard Y. Chang,et al.  ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide , 2015, Current protocols in molecular biology.

[32]  P. Sharpe,et al.  Expression analysis of candidate genes regulating successional tooth formation in the human embryo , 2014, Front. Physiol..

[33]  M. Shah,et al.  Generation of rodent and human osteoblasts. , 2014, BoneKEy reports.

[34]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[35]  A. Brechalov,et al.  Mammalian cells contain two functionally distinct PBAF complexes incorporating different isoforms of PHF10 signature subunit , 2014, Cell cycle.

[36]  H. Akiyama,et al.  Kruppel-like factor 4 attenuates osteoblast formation, function, and cross talk with osteoclasts , 2014, The Journal of cell biology.

[37]  G. Crabtree,et al.  Essential role of BRG, the ATPase subunit of BAF chromatin remodeling complexes, in leukemia maintenance. , 2014, Blood.

[38]  P. Varga-Weisz.  Chromatin remodeling: a collaborative effort , 2014, Nature Structural &Molecular Biology.

[39]  S. Elledge,et al.  Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome , 2013, Cell.

[40]  G. Crabtree,et al.  Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy , 2013, Nature Genetics.

[41]  David G Hendrickson,et al.  Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.

[42]  J. Reseland,et al.  Gene Expression Profiling during Murine Tooth Development , 2012, Front. Gene..

[43]  H. Stunnenberg,et al.  SS18 Together with Animal-Specific Factors Defines Human BAF-Type SWI/SNF Complexes , 2012, PloS one.

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

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

[46]  G. Stein,et al.  MicroRNA control of bone formation and homeostasis , 2012, Nature Reviews Endocrinology.

[47]  E. Moran,et al.  Essential Role of ARID2 Protein-containing SWI/SNF Complex in Tissue-specific Gene Expression* , 2011, The Journal of Biological Chemistry.

[48]  Florent Elefteriou,et al.  Genetic mouse models for bone studies--strengths and limitations. , 2011, Bone.

[49]  G. Stein,et al.  Epigenetic Regulation of Early Osteogenesis and Mineralized Tissue Formation by a HOXA10-PBX1-Associated Complex , 2011, Cells Tissues Organs.

[50]  Andre J. van Wijnen,et al.  A network connecting Runx2, SATB2, and the miR-23a∼27a∼24-2 cluster regulates the osteoblast differentiation program , 2010, Proceedings of the National Academy of Sciences.

[51]  Ming-Ming Zhou,et al.  Mechanism and Regulation of Acetylated Histone Binding by the Tandem PHD Finger of DPF3b , 2010, Nature.

[52]  S. Georgieva,et al.  Transcription coactivator SAYP combines chromatin remodeler Brahma and transcription initiation factor TFIID into a single supercomplex , 2009, Proceedings of the National Academy of Sciences.

[53]  B. Cairns,et al.  The biology of chromatin remodeling complexes. , 2009, Annual review of biochemistry.

[54]  Alexey I Nesvizhskii,et al.  An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency , 2009, Proceedings of the National Academy of Sciences.

[55]  Jeroen A. A. Demmers,et al.  The Transcriptional Coactivator SAYP Is a Trithorax Group Signature Subunit of the PBAP Chromatin Remodeling Complex , 2008, Molecular and Cellular Biology.

[56]  C. Allis,et al.  Chromatin remodeling and cancer, Part II: ATP-dependent chromatin remodeling. , 2007, Trends in molecular medicine.

[57]  R. Aebersold,et al.  An Essential Switch in Subunit Composition of a Chromatin Remodeling Complex during Neural Development , 2007, Neuron.

[58]  G. Stein,et al.  HOXA10 Controls Osteoblastogenesis by Directly Activating Bone Regulatory and Phenotypic Genes , 2007, Molecular and Cellular Biology.

[59]  Anne E Carpenter,et al.  A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen , 2006, Cell.

[60]  Yingnan Song,et al.  Making a tooth: growth factors, transcription factors, and stem cells , 2005, Cell Research.

[61]  M. Ermolaeva,et al.  A novel multidomain transcription coactivator SAYP can also repress transcription in heterochromatin , 2005, The EMBO journal.

[62]  T. Chi.  A BAF-centred view of the immune system , 2004, Nature Reviews Immunology.

[63]  G. Stein,et al.  Dlx3 Transcriptional Regulation of Osteoblast Differentiation: Temporal Recruitment of Msx2, Dlx3, and Dlx5 Homeodomain Proteins to Chromatin of the Osteocalcin Gene , 2004, Molecular and Cellular Biology.

[64]  P. Sassone-Corsi,et al.  ATF4 Is a Substrate of RSK2 and an Essential Regulator of Osteoblast Biology Implication for Coffin-Lowry Syndrome , 2004, Cell.

[65]  J. Vonesch,et al.  Tooth Morphogenesis and Pattern of Odontoblast Differentiation , 2003, Connective tissue research.

[66]  Shuo Chen,et al.  TGFβ-1 Downregulates DMP-1 and DSPP in Odontoblasts , 2002 .

[67]  R. Tjian,et al.  Selectivity of chromatin-remodelling cofactors for ligand-activated transcription , 2001, Nature.

[68]  P. Hanawalt,et al.  p53-Mediated DNA Repair Responses to UV Radiation: Studies of Mouse Cells Lacking p53, p21, and/orgadd45 Genes , 2000, Molecular and Cellular Biology.

[69]  William F. Morgan,et al.  Genomic instability in Gadd45a-deficient mice , 1999, Nature Genetics.

[70]  Luigi Naldini,et al.  Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo , 1997, Nature Biotechnology.

[71]  M. Yaniv,et al.  Purification and biochemical heterogeneity of the mammalian SWI‐SNF complex. , 1996, The EMBO journal.

[72]  G. Crabtree,et al.  Diversity and specialization of mammalian SWI/SNF complexes. , 1996, Genes & development.

[73]  Lynda F. Bonewald,et al.  Role of active and latent transforming growth factor β in bone formation , 1994 .

[74]  J. Wozney,et al.  Transforming Growth Factor-β Gene Family Members and Bone* , 1994 .

[75]  Paul A. Khavari,et al.  BRG1 contains a conserved domain of the SWI2/SNF2 family necessary for normal mitotic growth and transcription , 1993, Nature.

[76]  T. Wilanowski.  Krueppel-Like Factor 4 , 2020 .

[77]  Xuegong Zhang,et al.  DEGseq: an R package for identifying differentially expressed genes from RNA-seq data , 2010, Bioinform..

[78]  G. D. Pont.  A Collaborative Effort , 2010 .

[79]  P. Hanawalt,et al.  p 53-Mediated DNA Repair Responses to UV Radiation : Studies of Mouse Cells Lacking p 53 , p 21 , and / or gadd 45 Genes , 2000 .