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An Emerging Regulatory Landscape for Skeletal Development

https://doi.org/10.1016/j.tig.2016.10.001

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Genome‐Wide Mapping of DNA Hydroxymethylation in Osteoarthritic Chondrocytes

inferredcites →https://doi.org/10.1002/humu.22606openalex-snapshot

Identification of Novel Craniofacial Regulatory Domains Located far Upstream ofSOX9and Disrupted in Pierre Robin Sequence

inferredcites →https://doi.org/10.1002/jbmr.1945openalex-snapshot

An analysis of skeletal development in osteoblast-specific and chondrocyte-specific runt-related transcription factor-2 (Runx2) knockout mice

inferredcites →https://doi.org/10.1002/stem.1759openalex-snapshot

The Regulatory Landscape of Osteogenic Differentiation

inferredcites →https://doi.org/10.1007/s00412-016-0593-6openalex-snapshot

Chromosome conformation capture technologies and their impact in understanding genome function

inferredcites →https://doi.org/10.1007/s00774-002-0408-0openalex-snapshot

Requisite roles of Runx2 and Cbfb in skeletal development.

inferredcites →https://doi.org/10.1007/s00774-011-0273-9openalex-snapshot

Unraveling the transcriptional regulatory machinery in chondrogenesis

inferredcites →https://doi.org/10.1016/0968-0004(86)90226-4openalex-snapshot

Promoter-specific activation of RNA polymerase II transcription by Sp1

inferredcites →https://doi.org/10.1016/j.ajhg.2010.05.016openalex-snapshot

Identification of a Frameshift Mutation in Osterix in a Patient with Recessive Osteogenesis Imperfecta

inferredcites →https://doi.org/10.1016/j.bone.2015.04.035openalex-snapshot

Bone development

inferredcites →https://doi.org/10.1016/j.cell.2007.05.009openalex-snapshot

High-Resolution Profiling of Histone Methylations in the Human Genome

inferredcites →https://doi.org/10.1016/j.cell.2013.03.035openalex-snapshot

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

inferredcites →https://doi.org/10.1016/j.cell.2013.11.033openalex-snapshot

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

inferredcites →https://doi.org/10.1016/j.cell.2014.11.018openalex-snapshot

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

inferredcites →https://doi.org/10.1016/j.cell.2015.04.004openalex-snapshot

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

inferredcites →https://doi.org/10.1016/j.cell.2016.06.011openalex-snapshot

Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types

inferredcites →https://doi.org/10.1016/j.celrep.2015.06.013openalex-snapshot

Distinct Transcriptional Programs Underlie Sox9 Regulation of the Mammalian Chondrocyte

inferredcites →https://doi.org/10.1016/j.celrep.2016.04.043openalex-snapshot

Systematic Reconstruction of Molecular Cascades Regulating GP Development Using Single-Cell RNA-Seq

inferredcites →https://doi.org/10.1016/j.devcel.2005.02.013openalex-snapshot

Canonical Wnt/β-Catenin Signaling Prevents Osteoblasts from Differentiating into Chondrocytes

inferredcites →https://doi.org/10.1016/j.devcel.2005.03.016openalex-snapshot

Wnt/β-Catenin Signaling in Mesenchymal Progenitors Controls Osteoblast and Chondrocyte Differentiation during Vertebrate Skeletogenesis

inferredcites →https://doi.org/10.1016/j.devcel.2007.02.004openalex-snapshot

MEF2C Transcription Factor Controls Chondrocyte Hypertrophy and Bone Development

inferredcites →https://doi.org/10.1016/j.devcel.2010.07.010openalex-snapshot

Osteoblast Precursors, but Not Mature Osteoblasts, Move into Developing and Fractured Bones along with Invading Blood Vessels

inferredcites →https://doi.org/10.1016/j.devcel.2011.12.024openalex-snapshot

Sox9 Directs Hypertrophic Maturation and Blocks Osteoblast Differentiation of Growth Plate Chondrocytes

inferredcites →https://doi.org/10.1016/j.devcel.2016.04.002openalex-snapshot

Sp7/Osterix Is Restricted to Bone-Forming Vertebrates where It Acts as a Dlx Co-factor in Osteoblast Specification

inferredcites →https://doi.org/10.1016/j.gde.2016.06.012openalex-snapshot

Bone repair and stem cells

inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

inferredcites →https://doi.org/10.1016/j.molcel.2013.01.038openalex-snapshot

Modification of Enhancer Chromatin: What, How, and Why?

inferredcites →https://doi.org/10.1016/j.molcel.2014.06.015openalex-snapshot

Enhancer Function: Mechanistic and Genome-Wide Insights Come Together

inferredcites →https://doi.org/10.1016/j.molcel.2016.05.018openalex-snapshot

Chromatin Domains: The Unit of Chromosome Organization

inferredcites →https://doi.org/10.1016/j.molmed.2014.06.001openalex-snapshot

Osteoclasts: more than ‘bone eaters’

inferredcites →https://doi.org/10.1016/j.semcdb.2006.12.014openalex-snapshot

Enhancer identification through comparative genomics

inferredcites →https://doi.org/10.1016/j.tcb.2013.10.008openalex-snapshot

Distal enhancers: new insights into heart development and disease

inferredcites →https://doi.org/10.1016/j.ydbio.2015.01.022openalex-snapshot

BMP–Smad4 signaling is required for precartilaginous mesenchymal condensation independent of Sox9 in the mouse

inferredcites →https://doi.org/10.1016/j.ygeno.2015.06.003openalex-snapshot

Understanding how cis -regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences

inferredcites →https://doi.org/10.1016/s0092-8674(00)80257-3openalex-snapshot

Osf2/Cbfa1: A Transcriptional Activator of Osteoblast Differentiation

inferredcites →https://doi.org/10.1016/s0092-8674(00)80258-5openalex-snapshot

Targeted Disruption of Results in a Complete Lack of Bone Formation owing to Maturational Arrest of Osteoblasts

inferredcites →https://doi.org/10.1016/s0092-8674(00)80259-7openalex-snapshot

Cbfa1, a Candidate Gene for Cleidocranial Dysplasia Syndrome, Is Essential for Osteoblast Differentiation and Bone Development

inferredcites →https://doi.org/10.1016/s0092-8674(00)80260-3openalex-snapshot

Mutations Involving the Transcription Factor CBFA1 Cause Cleidocranial Dysplasia

inferredcites →https://doi.org/10.1016/s0092-8674(01)00622-5openalex-snapshot

The Novel Zinc Finger-Containing Transcription Factor Osterix Is Required for Osteoblast Differentiation and Bone Formation

inferredcites →https://doi.org/10.1016/s1534-5807(01)00003-xopenalex-snapshot

The Transcription Factors L-Sox5 and Sox6 Are Essential for Cartilage Formation

inferredcites →https://doi.org/10.1038/8792openalex-snapshot

Sox9 is required for cartilage formation

inferredcites →https://doi.org/10.1038/cr.2014.111openalex-snapshot

Osteogenic fate of hypertrophic chondrocytes

inferredcites →https://doi.org/10.1038/ejhg.2015.245openalex-snapshot

Genomic control process: development and evolution

inferredcites →https://doi.org/10.1038/nature07730openalex-snapshot

ChIP-seq accurately predicts tissue-specific activity of enhancers

inferredcites →https://doi.org/10.1038/nature09692openalex-snapshot

A unique chromatin signature uncovers early developmental enhancers in humans

inferredcites →https://doi.org/10.1038/nbt.1505openalex-snapshot

An integrated software system for analyzing ChIP-chip and ChIP-seq data

inferredcites →https://doi.org/10.1038/nbt.3450openalex-snapshot

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

inferredcites →https://doi.org/10.1038/ng.3097openalex-snapshot

Defining the role of common variation in the genomic and biological architecture of adult human height

inferredcites →https://doi.org/10.1038/ng0797-307openalex-snapshot

Missense mutations abolishing DNA binding of the osteoblast-specific transcription factor OSF2/CBFA1 in cleidocranial dysplasia

inferredcites →https://doi.org/10.1038/nmeth.1246openalex-snapshot

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

inferredcites →https://doi.org/10.1038/nmeth.2688openalex-snapshot

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

inferredcites →https://doi.org/10.1038/nprot.2012.101openalex-snapshot

Identifying ChIP-seq enrichment using MACS

inferredcites →https://doi.org/10.1038/nrendo.2016.71openalex-snapshot

Osteocytic signalling pathways as therapeutic targets for bone fragility

inferredcites →https://doi.org/10.1038/nrm3949openalex-snapshot

The selection and function of cell type-specific enhancers

inferredcites →https://doi.org/10.1038/sj.onc.1207676openalex-snapshot

Runx2 control of organization, assembly and activity of the regulatory machinery for skeletal gene expression

inferredcites →https://doi.org/10.1038/srep30558openalex-snapshot

Integrating Epigenomic Elements and GWASs Identifies BDNF Gene Affecting Bone Mineral Density and Osteoporotic Fracture Risk

inferredcites →https://doi.org/10.1073/pnas.0500031102openalex-snapshot

Bmpr1a and Bmpr1b have overlapping functions and are essential for chondrogenesis in vivo

inferredcites →https://doi.org/10.1073/pnas.0503617102openalex-snapshot

BMP signaling stimulates cellular differentiation at multiple steps during cartilage development

inferredcites →https://doi.org/10.1073/pnas.111092198openalex-snapshot

Haploinsufficiency of Sox9 results in defective cartilage primordia and premature skeletal mineralization

inferredcites →https://doi.org/10.1073/pnas.1302703111openalex-snapshot

Hypertrophic chondrocytes can become osteoblasts and osteocytes in endochondral bone formation

inferredcites →https://doi.org/10.1073/pnas.95.22.13030openalex-snapshot

The parathyroid hormone/parathyroid hormone-related peptide receptor coordinates endochondral bone development by directly controlling chondrocyte differentiation

inferredcites →https://doi.org/10.1074/jbc.m112.347716openalex-snapshot

Gli1 Protein Participates in Hedgehog-mediated Specification of Osteoblast Lineage during Endochondral Ossification

inferredcites →https://doi.org/10.1074/jbc.m112.409342openalex-snapshot

Hedgehog-Gli Activators Direct Osteo-chondrogenic Function of Bone Morphogenetic Protein toward Osteogenesis in the Perichondrium

inferredcites →https://doi.org/10.1074/jbc.m114.552216openalex-snapshot

The RUNX2 Cistrome in Osteoblasts

inferredcites →https://doi.org/10.1074/jbc.m114.578104openalex-snapshot

Genomic Determinants of Gene Regulation by 1,25-Dihydroxyvitamin D3 during Osteoblast-lineage Cell Differentiation

inferredcites →https://doi.org/10.1074/jbc.m115.648394openalex-snapshot

Selective Distal Enhancer Control of the Mmp13 Gene Identified through Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Genomic Deletions

inferredcites →https://doi.org/10.1074/jbc.m116.736538openalex-snapshot

Epigenetic Plasticity Drives Adipogenic and Osteogenic Differentiation of Marrow-derived Mesenchymal Stem Cells

inferredcites →https://doi.org/10.1074/jbc.m303471200openalex-snapshot

Transcriptional Co-activators CREB-binding Protein and p300 Regulate Chondrocyte-specific Gene Expression via Association with Sox9

inferredcites →https://doi.org/10.1074/jbc.m502409200openalex-snapshot

Sox9 and p300 Cooperatively Regulate Chromatin-mediated Transcription

inferredcites →https://doi.org/10.1080/03008207.2016.1183667openalex-snapshot

SOX9 and the many facets of its regulation in the chondrocyte lineage

inferredcites →https://doi.org/10.1091/mbc.e08-03-0329openalex-snapshot

CCAAT/Enhancer-binding Protein β Promotes Osteoblast Differentiation by Enhancing Runx2 Activity with ATF4

inferredcites →https://doi.org/10.1093/emboj/17.19.5718openalex-snapshot

A new long form of Sox5 (L‐Sox5), Sox6 and Sox9 are coexpressed in chondrogenesis and cooperatively activate the type II collagen gene

inferredcites →https://doi.org/10.1093/hmg/ddg158openalex-snapshot

Loss of DNA-dependent dimerization of the transcription factor SOX9 as a cause for campomelic dysplasia

inferredcites →https://doi.org/10.1093/hmg/ddg182openalex-snapshot

Dimerization of SOX9 is required for chondrogenesis, but not for sex determination

inferredcites →https://doi.org/10.1093/nar/gkv426openalex-snapshot

The SOX9 upstream region prone to chromosomal aberrations causing campomelic dysplasia contains multiple cartilage enhancers

inferredcites →https://doi.org/10.1093/nar/gkv688openalex-snapshot

The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis

inferredcites →https://doi.org/10.1101/cshperspect.a008334openalex-snapshot

Development of the Endochondral Skeleton

inferredcites →https://doi.org/10.1101/gad.1017802openalex-snapshot

The transcription factor Sox9 has essential roles in successive steps of the chondrocyte differentiation pathway and is required for expression of Sox5 and Sox6

inferredcites →https://doi.org/10.1101/gad.1171104openalex-snapshot

Interactions between Sox9 and β-catenin control chondrocyte differentiation

inferredcites →https://doi.org/10.1101/gad.1174704openalex-snapshot

Runx2 and Runx3 are essential for chondrocyte maturation, and Runx2 regulates limb growth through induction of Indian hedgehog

inferredcites →https://doi.org/10.1101/gad.13.16.2072openalex-snapshot

Indian hedgehog signaling regulates proliferation and differentiation of chondrocytes and is essential for bone formation

inferredcites →https://doi.org/10.1101/gad.988402openalex-snapshot

The Dlx5 and Dlx6 homeobox genes are essential for craniofacial, axial, and appendicular skeletal development

inferredcites →https://doi.org/10.1111/j.1749-6632.1996.tb56252.xopenalex-snapshot

Campomelic Dysplasia with XY Sex Reversal: Diverse Phenotypes Resulting from Mutations in a Single Genea

inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

inferredcites →https://doi.org/10.1126/science.1256271openalex-snapshot

Chromatin state dynamics during blood formation

inferredcites →https://doi.org/10.1126/science.273.5275.613openalex-snapshot

Regulation of Rate of Cartilage Differentiation by Indian Hedgehog and PTH-Related Protein

inferredcites →https://doi.org/10.1128/mcb.00695-08openalex-snapshot

L-Sox5 and Sox6 Drive Expression of the Aggrecan Gene in Cartilage by Securing Binding of Sox9 to a Far-Upstream Enhancer

inferredcites →https://doi.org/10.1128/mcb.15.4.1858openalex-snapshot

Two Distinct Osteoblast-Specific cis-Acting Elements Control Expression of a Mouse Osteocalcin Gene

inferredcites →https://doi.org/10.1146/annurev.genom.9.081307.164437openalex-snapshot

Transcriptional Control of Skeletogenesis

inferredcites →https://doi.org/10.1159/000350089openalex-snapshot

Sox9 Modulates Proliferation and Expression of Osteogenic Markers of Adipose-Derived Stem Cells (ASC)

inferredcites →https://doi.org/10.1172/jci11706openalex-snapshot

Indian hedgehog couples chondrogenesis to osteogenesis in endochondral bone development

inferredcites →https://doi.org/10.1186/1471-2164-14-105openalex-snapshot

Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells

inferredcites →https://doi.org/10.1186/gb-2014-15-3-r52openalex-snapshot

Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis

inferredcites →https://doi.org/10.1242/bio.201411031openalex-snapshot

Dual pathways to endochondral osteoblasts: a novel chondrocyte-derived osteoprogenitor cell identified in hypertrophic cartilage

inferredcites →https://doi.org/10.1242/dev.01006openalex-snapshot

Ihh signaling is directly required for the osteoblast lineage in the endochondral skeleton

inferredcites →https://doi.org/10.1242/dev.02480openalex-snapshot

Distinct roles for Hedgehog and canonical Wnt signaling in specification,differentiation and maintenance of osteoblast progenitors

inferredcites →https://doi.org/10.1242/dev.029926openalex-snapshot

BMP canonical Smad signaling through Smad1 and Smad5 is required for endochondral bone formation

inferredcites →https://doi.org/10.1242/dev.057802openalex-snapshot

Sox9 sustains chondrocyte survival and hypertrophy in part through Pik3ca-Akt pathways

inferredcites →https://doi.org/10.1242/dev.129.12.2977openalex-snapshot

PTHrP and Indian hedgehog control differentiation of growth plate chondrocytes at multiple steps

inferredcites →https://doi.org/10.1242/dev.134502openalex-snapshot

AP-1 family members act with Sox9 to promote chondrocyte hypertrophy

inferredcites →https://doi.org/10.1371/journal.pgen.1004423openalex-snapshot

Phenotypic Dissection of Bone Mineral Density Reveals Skeletal Site Specificity and Facilitates the Identification of Novel Loci in the Genetic Regulation of Bone Mass Attainment

inferredcites →https://doi.org/10.1371/journal.pone.0004543openalex-snapshot

C/EBPβ Promotes Transition from Proliferation to Hypertrophic Differentiation of Chondrocytes through Transactivation of p57Kip2

inferredcites →https://doi.org/10.1371/journal.pone.0107577openalex-snapshot

SOX9 Regulates Multiple Genes in Chondrocytes, Including Genes Encoding ECM Proteins, ECM Modification Enzymes, Receptors, and Transporters

inferredcites →https://doi.org/10.1371/journal.pone.0148619openalex-snapshot

Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Cross-Validation of Conserved Osteoblast-Specific Enhancers Illuminates Bone Diseases and Early Skeletal Evolution

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Expression and Transcriptional Targets of TGFβ ‐ RII in Paracentrotus lividus Larval Skeletogenesis

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Single Cell Omics for Musculoskeletal Research

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Osteoclast-derived exosomal miR-212-3p suppressed the anabolism and accelerated the catabolism of chondrocytes in osteoarthritis by targeting TGF-β1/Smad2 signaling

inferred← citeshttps://doi.org/10.1016/j.cdev.2024.203924openalex-snapshot

Xenopus tropicalis osteoblast-specific open chromatin regions reveal promoters and enhancers involved in human skeletal phenotypes and shed light on early vertebrate evolution

inferred← citeshttps://doi.org/10.1016/j.coisb.2018.08.005openalex-snapshot

RNA language in Caenorhabditis elegans and bacteria interspecies communication and memory

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MEF2D as a key regulator of osteoarthritis with exploratory therapeutic potential

inferred← citeshttps://doi.org/10.1016/j.jtbi.2022.111005openalex-snapshot

Theoretical evidence of osteoblast self-inhibition after activation of the genetic regulatory network controlling mineralization

inferred← citeshttps://doi.org/10.1016/j.jtbi.2025.112284openalex-snapshot

Stiffness-sensitive gene regulation in human mesenchymal stem cells: Modelling mechanotransduction to predict mineralization and bone protein expression

inferred← citeshttps://doi.org/10.1016/j.mbplus.2021.100088openalex-snapshot

Runx2 is required for hypertrophic chondrocyte mediated degradation of cartilage matrix during endochondral ossification

inferred← citeshttps://doi.org/10.1093/jbmr/zjae178openalex-snapshot

Modeling of skeletal development and diseases using human pluripotent stem cells

inferred← citeshttps://doi.org/10.1101/2022.12.21.521381openalex-snapshot

ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

inferred← citeshttps://doi.org/10.1101/2023.08.30.555543openalex-snapshot

Architecture and evolutionary conservation of Xenopus tropicalis osteoblast-specific regulatory regions shed light on bone diseases and early skeletal evolution

inferred← citeshttps://doi.org/10.1111/ocr.12171openalex-snapshot

Moving towards precision orthodontics: An evolving paradigm shift in the planning and delivery of customized orthodontic therapy

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An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos

inferred← citeshttps://doi.org/10.12688/f1000research.17471.1openalex-snapshot

Recent advances in understanding the regulation of metalloproteinases

inferred← citeshttps://doi.org/10.1371/journal.pgen.1007346openalex-snapshot

Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2912945/v1openalex-snapshot

Predicting Bone Protein Expression: A Stiffness-Dependent Gene Regulation Model

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RNA splicing in bone diseases: mechanisms, pathogenesis and therapeutics

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The Evolution of Biomineralization through the Co-Option of Organic Scaffold Forming Networks

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Inhibiting the integrated stress response pathway prevents aberrant chondrocyte differentiation thereby alleviating chondrodysplasia

inferred← citeshttps://doi.org/10.7554/elife.89080openalex-snapshot

ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

inferred← citeshttps://doi.org/10.7554/elife.89080.1openalex-snapshot

Actomyosin remodeling regulates biomineral formation, growth and morphology during eukaryote skeletogenesis

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ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

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ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

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ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

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