MBD3 [The Human Chemical-Genetic Interaction Map Project]

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======= MBD3 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: MBD3
  * **<color #00a2e8>Official Name</color>**: methyl-CpG binding domain protein 3
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=53615|53615]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/O95983|O95983]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=MBD3&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20MBD3|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/603573|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. This gene belongs to a family of nuclear proteins which are characterized by the presence of a methyl-CpG binding domain (MBD). The encoded protein is a subunit of the NuRD, a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. Unlike the other family members, the encoded protein is not capable of binding to methylated DNA. The protein mediates the association of metastasis-associated protein 2 with the core histone deacetylase complex. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Acts as transcriptional repressor and plays a role in gene silencing. Does not bind to DNA by itself (PubMed:12124384). Binds to DNA with a preference for sites containing methylated CpG dinucleotides (in vitro). Binds to a lesser degree DNA containing unmethylated CpG dinucleotides (PubMed:24307175). Recruits histone deacetylases and DNA methyltransferases. {ECO:0000269|PubMed:10947852, ECO:0000269|PubMed:12124384, ECO:0000269|PubMed:18644863, ECO:0000269|PubMed:23361464, ECO:0000269|PubMed:24307175, ECO:0000269|PubMed:9774669}.

<button type='primary' size='sm' modal='Pfam_Domains'>Pfam Domains</button>
<button type='primary' size='sm' modal='GO_terms'>GO Terms</button>


<modal id='Pfam_Domains' size='lg' title='Pfam Domains'>
|MBD|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|methylation-dependent chromatin silencing|
|NuRD complex|
|regulation of DNA methylation|
|heterochromatin|
|methyl-CpG binding|
|nucleosomal DNA binding|
|chromatin silencing|
|chromatin organization involved in negative regulation of transcription|
|chromatin organization involved in regulation of transcription|
|ATP-dependent chromatin remodeling|
|negative regulation of gene expression, epigenetic|
|RNA polymerase II distal enhancer sequence-specific DNA binding|
|histone acetylation|
|internal peptidyl-lysine acetylation|
|peptidyl-lysine acetylation|
|internal protein amino acid acetylation|
|response to estradiol|
|protein acetylation|
|gene silencing|
|chromatin remodeling|
|regulation of signal transduction by p53 class mediator|
|protein acylation|
|regulation of gene expression, epigenetic|
|nuclear chromatin|
|aging|
|peptidyl-lysine modification|
|regulation of DNA metabolic process|
|histone modification|
|covalent chromatin modification|
|in utero embryonic development|
|embryonic organ development|
|response to nutrient levels|
|RNA polymerase II proximal promoter sequence-specific DNA binding|
|heart development|
|response to extracellular stimulus|
|protein-containing complex|
|chordate embryonic development|
|embryo development ending in birth or egg hatching|
|chromatin organization|
|brain development|
|head development|
|response to lipid|
|negative regulation of transcription by RNA polymerase II|
|circulatory system development|
|peptidyl-amino acid modification|
|response to hormone|
|response to organic cyclic compound|
|embryo development|
|central nervous system development|
|chromosome organization|
|negative regulation of transcription, DNA-templated|
|negative regulation of nucleic acid-templated transcription|
|negative regulation of RNA biosynthetic process|
|negative regulation of RNA metabolic process|
|negative regulation of cellular macromolecule biosynthetic process|
|negative regulation of nucleobase-containing compound metabolic process|
|DNA binding|
|negative regulation of macromolecule biosynthetic process|
|response to endogenous stimulus|
|negative regulation of cellular biosynthetic process|
|negative regulation of biosynthetic process|
|response to oxygen-containing compound|
|negative regulation of gene expression|
|tissue development|
|regulation of intracellular signal transduction|
</modal>
\\

 === CRISPR Data ===
<button type='primary' size='small' modal='Compound_Hit'>Compound Hit</button>
<button type='primary' size='small' modal='Most_Correlated_Genes'>Most Correlated Genes in Chemogenomics</button>
<button type='primary' size='small' modal='Essential_Avana'>Tissues where Essential in the Avana Dataset (DepMap 20Q1)</button>

<modal id='Compound_Hit' size='lg' title='Compound Hit'>
^Screen^Score^
|[[:results:exp36|TRAIL 50ng/ml R00 exp36]]|-3.2|
|[[:results:exp35|TRAIL 5ng/ml R00 exp35]]|-2.26|
|[[:results:exp443|SNS-032 15μM R08 exp443]]|-2.06|
|[[:results:exp435|JQ1 0.8μM R08 exp435]]|-2|
|[[:results:exp264|Arsenate 40μM R06 exp264]]|-1.84|
|[[:results:exp34|Rotenone 20μM R00 exp34]]|-1.77|
|[[:results:exp102|Nifuroxazide 5μM R03 exp102]]|1.7|
|[[:results:exp233|EPZ-5676 30μM R05 exp233]]|1.72|
|[[:results:exp413|THZ531 0.11 to 0.175μM on day4 R07 exp413]]|1.76|
|[[:results:exp234|Ethanol 0.01 R05 exp234]]|1.84|
|[[:results:exp274|Citral 50μM R06 exp274]]|1.92|
|[[:results:exp510|Nicotine 3000μM R08 exp510]]|2.1|
|[[:results:exp21|MLN-4924 0.2μM R00 exp21]]|2.22|
|[[:results:exp269|Bisphenol A 100μM R06 exp269]]|2.28|
|[[:results:exp500|LY2090314 0.003μM R08 exp500 no dilution day6]]|2.59|
|[[:results:exp499|LY2090314 0.003μM R08 exp499]]|2.93|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:m:mta2|MTA2]]|0.56|
|[[:human genes:g:gatad2a|GATAD2A]]|0.431|
|[[:human genes:g:gatad2b|GATAD2B]]|0.408|
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 0/726
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|0/28|
|blood|0/28|
|bone|0/25|
|breast|0/33|
|central nervous system|0/56|
|cervix|0/4|
|colorectal|0/17|
|esophagus|0/13|
|fibroblast|0/1|
|gastric|0/15|
|kidney|0/21|
|liver|0/20|
|lung|0/75|
|lymphocyte|0/14|
|ovary|0/26|
|pancreas|0/24|
|peripheral nervous system|0/16|
|plasma cell|0/15|
|prostate|0/1|
|skin|0/24|
|soft tissue|0/7|
|thyroid|0/2|
|upper aerodigestive|0/22|
|urinary tract|0/29|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 13941
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 6.83 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='MBD3 Expression in NALM6 Cells: 6.83'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>