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ONTOLOGY REPORT - ANNOTATIONS


Term:chromatin organization involved in negative regulation of transcription
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Accession:GO:0097549 term browser browse the term
Definition:Any process that stops, prevents, or reduces the frequency, rate or extent of transcription by chromatin organization.
Synonyms:exact_synonym: negative regulation of transcription by chromatin organization
 narrow_synonym: negative regulation of gene-specific transcription from RNA polymerase II promoter by histone modification;   negative regulation of global transcription from Pol II promoter by histone modification;   negative regulation of transcription from Pol II promoter by histone modification;   negative regulation of transcription from RNA polymerase II promoter by histone modification;   negative regulation of transcription from RNA polymerase II promoter, global by histone modification
 alt_id: GO:1903758


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chromatin silencing term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07062859.1 RGD:13792537
G Bmi1 BMI1 proto-oncogene, polycomb ring finger JBrowse link 17 85,360,439 85,370,283 RGD:13792537
G Ctbp1 C-terminal binding protein 1 JBrowse link 14 82,762,109 82,789,350 RGD:1600115
RGD:1624291
G Eed embryonic ectoderm development JBrowse link 1 154,189,252 154,216,340 RGD:13792537
G H1f0 H1 histone family, member 0 JBrowse link 7 120,260,776 120,262,636 RGD:1624291
G H2ac1 H2A clustered histone 1 JBrowse link 17 43,422,454 43,422,846 RGD:13792537
G H2ac20 H2A clustered histone 20 JBrowse link 2 198,360,271 198,360,735 RGD:13792537
G H2ac21 H2A clustered histone 21 JBrowse link 2 198,359,754 198,360,146 RGD:13792537
G H2afb3 H2A histone family, member B3 JBrowse link X 88,602,135 88,602,485 RGD:13792537
G H2aj H2A.J histone JBrowse link 4 170,766,900 170,767,384 RGD:13792537
G H2ax H2A.X variant histone JBrowse link 8 48,665,652 48,666,981 RGD:13792537
G H2az1 H2A.Z variant histone 1 JBrowse link 2 243,105,224 243,107,333 RGD:13792537
G H2az2 H2A.Z variant histone 2 JBrowse link 14 86,687,782 86,706,639 RGD:13792537
G Hells helicase, lymphoid specific JBrowse link 1 257,901,856 257,953,889 RGD:1624291
G Hils1 histone linker H1 domain, spermatid-specific 1 JBrowse link 10 82,775,691 82,776,487 RGD:1624291
G Hist1h2ac histone cluster 1 H2A family member C JBrowse link 17 44,520,484 44,521,142 RGD:13792537
G Hist1h2af histone cluster 1 H2A family member F JBrowse link 17 43,627,237 43,627,629 RGD:13792537
G Hist1h2ah histone cluster 1 H2A family member H JBrowse link 17 43,632,354 43,632,851 RGD:13792537
G Hist1h2ai histone cluster 1, H2ai JBrowse link 17 44,758,412 44,759,675 RGD:13792537
G hist1h2ail2 histone cluster 1, H2ai-like2 JBrowse link 17 44,794,087 44,794,563 RGD:13792537
G Hist1h2ak histone cluster 1, H2ak JBrowse link 17 44,840,990 44,841,382 RGD:13792537
G Hist1h2an histone cluster 1, H2an JBrowse link 17 43,779,174 43,779,775 RGD:13792537
G Hist1h2ao histone cluster 1, H2ao JBrowse link 17 44,744,534 44,744,931 RGD:13792537
G Hist2h2aa2 histone cluster 2 H2A family member A2 JBrowse link 2 198,381,678 198,382,247 RGD:13792537
G Hist2h2aa3 histone cluster 2 H2A family member A3 JBrowse link 2 198,388,766 198,389,293 RGD:13792537
G Hist3h2a histone cluster 3, H2a JBrowse link 10 45,297,603 45,299,155 RGD:13792537
G Hmgb1 high mobility group box 1 JBrowse link 12 7,082,529 7,090,246 RGD:1624291
G Hypm huntingtin interacting protein M JBrowse link X 13,989,401 13,989,955 RGD:13792537
G Kdm1a lysine demethylase 1A JBrowse link 5 154,909,003 154,965,171 RGD:1624291
G Kmt2d lysine methyltransferase 2D JBrowse link 7 140,507,137 140,542,479 RGD:1624291
G LOC100363125 rCG42854-like JBrowse link X 13,991,860 13,992,606 RGD:13792537
G LOC100910554 histone H2A type 1-like JBrowse link 17 44,738,552 44,739,195 RGD:13792537
G LOC103690002 histone H2A.J JBrowse link 4 170,148,955 170,149,479 RGD:13792537
G LOC103690190 histone H2A type 1-E JBrowse link 17 44,747,686 44,748,229 RGD:13792537
G LOC103692167 polycomb group RING finger protein 1 JBrowse link 4 114,776,680 114,779,447 RGD:13792537
G LOC680063 similar to histone 2a RGD:13792537
G LOC680322 similar to Histone H2A type 1 JBrowse link 17 44,527,990 44,528,557 RGD:13792537
G LOC684773 similar to histone 2a JBrowse link 17 43,777,353 43,777,827 RGD:13792537
G Macroh2a1 macroH2A.1 histone JBrowse link 17 9,282,109 9,344,698 RGD:13792537
G Macroh2a2 macroH2A.2 histone JBrowse link 20 31,352,924 31,402,483 RGD:13792537
G Mecp2 methyl CpG binding protein 2 JBrowse link X 156,650,389 156,713,813 RGD:1624291
RGD:1600115
G Morf4l1 mortality factor 4 like 1 JBrowse link 8 97,473,454 97,494,974 RGD:13792537
G Morf4l2 mortality factor 4 like 2 JBrowse link X 107,394,468 107,405,564 RGD:13792537
G Msl3 MSL complex subunit 3 JBrowse link X 27,015,826 27,033,562 RGD:13792537
G Msl3l2 male-specific lethal 3-like 2 (Drosophila) JBrowse link 20 37,580,002 37,590,015 RGD:13792537
G Pcgf1 polycomb group ring finger 1 JBrowse link 4 113,911,129 113,913,718 RGD:13792537
G Pcgf2 polycomb group ring finger 2 JBrowse link 10 85,631,829 85,642,591 RGD:13792537
G Ppm1d protein phosphatase, Mg2+/Mn2+ dependent, 1D JBrowse link 10 72,909,550 72,945,884 RGD:1624291
G RGD1562306 similar to H2A histone family, member Z JBrowse link 6 11,859,622 11,860,016 RGD:13792537
G RGD1562871 similar to BMI1-like protein JBrowse link X 79,546,624 79,547,767 RGD:13792537
G Tnp1 transition protein 1 JBrowse link 9 80,294,837 80,295,446 RGD:1624291
RGD:1600115
G Ubr2 ubiquitin protein ligase E3 component n-recognin 2 JBrowse link 9 16,003,058 16,080,152 RGD:1624291
RGD:13792537
chromatin silencing at telomere term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dot1l DOT1 like histone lysine methyltransferase JBrowse link 7 11,786,105 11,824,742 RGD:13792537
G Dpy30 dpy-30 histone methyltransferase complex regulatory subunit JBrowse link 6 22,296,128 22,316,894 RGD:13792537
G Dydc1 DPY30 domain containing 1 JBrowse link 16 18,648,030 18,667,962 RGD:13792537
G Dydc2 DPY30 domain containing 2 JBrowse link 16 18,635,235 18,649,074 RGD:13792537
G Ezh1 enhancer of zeste 1 polycomb repressive complex 2 subunit JBrowse link 10 89,104,026 89,139,978 RGD:1624291
G Ezh2 enhancer of zeste 2 polycomb repressive complex 2 subunit JBrowse link 4 77,284,404 77,347,011 RGD:1624291
G Hat1 histone acetyltransferase 1 JBrowse link 3 58,022,395 58,070,067 RGD:1600115
G Rif1 replication timing regulatory factor 1 JBrowse link 3 37,599,540 37,648,818 RGD:1624291
DNA methylation-dependent heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnmt3a DNA methyltransferase 3 alpha JBrowse link 6 28,205,375 28,346,052 RGD:1624291
G Dnmt3b DNA methyltransferase 3 beta JBrowse link 3 149,131,541 149,170,061 RGD:1624291
G Hdac1 histone deacetylase 1 JBrowse link 5 147,716,664 147,743,723 RGD:1624291
G Hells helicase, lymphoid specific JBrowse link 1 257,901,856 257,953,889 RGD:1624291
RGD:13792537
G LOC100911660 lymphocyte-specific helicase-like JBrowse link 1 257,614,688 257,660,184 RGD:13792537
G Mbd2 methyl-CpG binding domain protein 2 JBrowse link 18 65,814,026 65,885,115 RGD:1624291
G Mbd3 methyl-CpG binding domain protein 3 JBrowse link 7 12,179,046 12,186,251 RGD:1624291
G Smarca4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 JBrowse link 8 22,648,323 22,739,468 RGD:1624291
heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07027368.1 RGD:13792537
G Bahd1 bromo adjacent homology domain containing 1 JBrowse link 3 110,708,790 110,732,038 RGD:1624291
G Baz2a bromodomain adjacent to zinc finger domain, 2A JBrowse link 7 2,518,267 2,548,840 RGD:1624291
G Ezh1 enhancer of zeste 1 polycomb repressive complex 2 subunit JBrowse link 10 89,104,026 89,139,978 RGD:1624291
G Hmga2 high mobility group AT-hook 2 JBrowse link 7 65,159,944 65,275,408 RGD:1624291
RGD:1600115
G LOC100362333 DNA-directed DNA polymerase epsilon 3 JBrowse link 7 118,816,053 118,816,725 RGD:13792537
G Pole3 DNA polymerase epsilon 3, accessory subunit JBrowse link 5 78,380,813 78,384,047 RGD:13792537
G Sirt1 sirtuin 1 JBrowse link 20 26,831,971 26,851,587 RGD:1624291
heterochromatin assembly by small RNA term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Fam172a family with sequence similarity 172, member A JBrowse link 2 4,942,795 5,547,744 RGD:13792537
G Nrde2 NRDE-2, necessary for RNA interference, domain containing JBrowse link 6 124,136,949 124,177,426 RGD:13792537
G Znfx1 zinc finger, NFX1-type containing 1 JBrowse link 3 163,787,101 163,847,671 RGD:13792537
heterochromatin maintenance term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Arid1a AT-rich interaction domain 1A JBrowse link 5 151,904,687 151,977,973 RGD:1624291
G Hdac2 histone deacetylase 2 JBrowse link 20 43,084,870 43,108,198 RGD:1624291
G Mthfr methylenetetrahydrofolate reductase JBrowse link 5 164,844,642 164,864,360 RGD:1624291
G Sirt1 sirtuin 1 JBrowse link 20 26,831,971 26,851,587 RGD:1624291
G Ube2b ubiquitin-conjugating enzyme E2B JBrowse link 10 37,439,947 37,454,867 RGD:1624291
G Wdhd1 WD repeat and HMG-box DNA binding protein 1 JBrowse link 15 24,021,674 24,056,073 RGD:1624291
heterochromatin organization involved in chromatin silencing term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Smchd1 structural maintenance of chromosomes flexible hinge domain containing 1 JBrowse link 9 119,675,750 119,818,620 RGD:1624291
inactivation of X chromosome by heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Smchd1 structural maintenance of chromosomes flexible hinge domain containing 1 JBrowse link 9 119,675,750 119,818,620 RGD:1624291
negative regulation of chromatin silencing term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Atad2 ATPase family, AAA domain containing 2 JBrowse link 7 97,984,754 98,027,379 RGD:13792537
G Atad2b ATPase family, AAA domain containing 2B JBrowse link 6 28,998,080 29,066,850 RGD:13792537
G H1f0 H1 histone family, member 0 JBrowse link 7 120,260,776 120,262,636 RGD:13792537
G H1f1 H1.1 linker histone, cluster member JBrowse link 17 43,614,101 43,614,844 RGD:13792537
G H1f10 H1.10 linker histone JBrowse link 4 119,889,016 119,892,661 RGD:13792537
G H1f2 H1.2 linker histone, cluster member JBrowse link 17 43,638,938 43,640,445 RGD:13792537
G H1f4 H1.4 linker histone, cluster member JBrowse link 17 43,734,461 43,735,120 RGD:13792537
G H1f5 H1.5 linker histone, cluster member JBrowse link 17 44,766,313 44,766,981 RGD:13792537
G H1f6 H1.6 linker histone, cluster member JBrowse link 17 43,675,190 43,675,934 RGD:13792537
G H1f8 H1.8 linker histone JBrowse link 4 147,844,658 147,849,779 RGD:13792537
G H4f3 H1.3 linker histone, cluster member JBrowse link 17 43,797,711 43,798,450 RGD:13792537
G Hils1 histone linker H1 domain, spermatid-specific 1 JBrowse link 10 82,775,691 82,776,487 RGD:13792537
negative regulation of DNA methylation-dependent heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Aicda activation-induced cytidine deaminase JBrowse link 4 155,359,909 155,371,104 RGD:1624291
G Apobec1 apolipoprotein B mRNA editing enzyme catalytic subunit 1 JBrowse link 4 155,386,367 155,414,034 RGD:1624291
RGD:1600115
G Tet1 tet methylcytosine dioxygenase 1 JBrowse link 20 27,359,122 27,438,039 RGD:1624291
negative regulation of ribosomal DNA heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Phf2 PHD finger protein 2 JBrowse link 17 16,240,458 16,274,626 RGD:1624291
G Phf8 PHD finger protein 8 JBrowse link X 21,063,487 21,168,750 RGD:1624291
pericentric heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cenpv centromere protein V JBrowse link 10 48,846,513 48,861,893 RGD:1624291
RGD:13792537
G Dicer1 dicer 1 ribonuclease III JBrowse link 6 128,388,084 128,453,234 RGD:1624291
G H3f3a H3 histone family member 3A JBrowse link 13 99,091,246 99,102,828 RGD:1624291
G H3f3b H3 histone family member 3B JBrowse link 10 104,573,666 104,575,890 RGD:1624291
G Hells helicase, lymphoid specific JBrowse link 1 257,901,856 257,953,889 RGD:1624291
RGD:13792537
G LOC100911660 lymphocyte-specific helicase-like JBrowse link 1 257,614,688 257,660,184 RGD:13792537
G Znfx1 zinc finger, NFX1-type containing 1 JBrowse link 3 163,787,101 163,847,671 RGD:13792537
positive regulation of chromatin silencing term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Mier1 MIER1 transcriptional regulator JBrowse link 5 122,642,065 122,693,642 RGD:1624291
G Sin3a SIN3 transcription regulator family member A JBrowse link 8 61,748,590 61,803,314 RGD:1624291
G Sirt1 sirtuin 1 JBrowse link 20 26,831,971 26,851,587 RGD:1600115
positive regulation of chromatin silencing at telomere term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Sirt6 sirtuin 6 JBrowse link 7 10,937,622 10,943,048 RGD:1624291
positive regulation of DNA methylation-dependent heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Atf7ip activating transcription factor 7 interacting protein JBrowse link 4 170,476,998 170,563,063 RGD:1624291
G Dnmt1 DNA methyltransferase 1 JBrowse link 8 21,922,515 21,968,495 RGD:1600115
RGD:1624291
G Morc2 MORC family CW-type zinc finger 2 JBrowse link 14 83,889,138 83,930,263 RGD:1624291
G Mphosph8 M-phase phosphoprotein 8 JBrowse link 15 36,918,843 36,946,712 RGD:1600115
RGD:1624291
G Pphln1 periphilin 1 JBrowse link 7 134,602,109 134,693,807 RGD:1624291
G Resf1 retroelement silencing factor 1 JBrowse link 4 183,879,177 183,905,807 RGD:1624291
G Setdb1 SET domain bifurcated histone lysine methyltransferase 1 JBrowse link 2 196,495,867 196,527,412 RGD:1624291
RGD:13792537
G Setdb2 SET domain bifurcated histone lysine methyltransferase 2 JBrowse link 15 38,699,135 39,745,035 RGD:13792537
G Tasor transcription activation suppressor JBrowse link 16 3,050,506 3,108,168 RGD:1624291
G Trim28 tripartite motif-containing 28 JBrowse link 1 65,544,369 65,551,043 RGD:1624291
RGD:1600115
positive regulation of heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Tpr translocated promoter region, nuclear basket protein JBrowse link 13 67,611,685 67,672,833 RGD:1624291
RGD:1600115
positive regulation of subtelomeric heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Sirt6 sirtuin 6 JBrowse link 7 10,937,622 10,943,048 RGD:1624291
rDNA heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Baz2a bromodomain adjacent to zinc finger domain, 2A JBrowse link 7 2,518,267 2,548,840 RGD:1624291
G Bend3 BEN domain containing 3 JBrowse link 20 48,248,193 48,270,905 RGD:1624291
RGD:13792537
G Rrp8 ribosomal RNA processing 8 JBrowse link 1 170,574,670 170,578,693 RGD:1624291
RGD:13792537
RGD:1600115
G Sirt1 sirtuin 1 JBrowse link 20 26,831,971 26,851,587 RGD:1624291
RGD:1600115
G Smarca5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 JBrowse link 19 30,936,703 30,969,454 RGD:1624291
G Suv39h1 suppressor of variegation 3-9 homolog 1 JBrowse link X 146,532,002 146,533,538 RGD:1624291
G Suv39h1l1 suppressor of variegation 3-9 homolog 1 (Drosophila)-like 1 JBrowse link X 15,171,280 15,185,191 RGD:1600115
G Ubtf upstream binding transcription factor JBrowse link 10 90,250,275 90,265,772 RGD:1624291
regulation of chromatin silencing term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Hira histone cell cycle regulator JBrowse link 11 86,168,196 86,276,430 RGD:13792537
G LOC100911837 protein HIRA-like JBrowse link 11 85,802,536 85,896,680 RGD:13792537
G Uty ubiquitously transcribed tetratricopeptide repeat containing, Y-linked JBrowse link Y 1,065,274 1,206,127 RGD:1624291
regulation of chromatin silencing at telomere term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cdc45 cell division cycle 45 JBrowse link 11 86,328,785 86,354,099 RGD:13792537
regulation of DNA methylation-dependent heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Pou5f1 POU class 5 homeobox 1 JBrowse link 20 3,747,231 3,751,994 RGD:1624291
regulation of ribosomal DNA heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Macroh2a1 macroH2A.1 histone JBrowse link 17 9,282,109 9,344,698 RGD:1624291
G Naa40 N(alpha)-acetyltransferase 40, NatD catalytic subunit JBrowse link 1 222,478,021 222,495,382 RGD:13792537
senescence-associated heterochromatin focus assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cdkn2a cyclin-dependent kinase inhibitor 2A JBrowse link 5 107,823,323 107,832,405 RGD:1624291
G Hmga1 high mobility group AT-hook 1 JBrowse link 20 7,132,501 7,140,155 RGD:1624291
RGD:1600115
G Hmga2 high mobility group AT-hook 2 JBrowse link 7 65,159,944 65,275,408 RGD:1624291
RGD:1600115
subtelomeric heterochromatin assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G H3f3a H3 histone family member 3A JBrowse link 13 99,091,246 99,102,828 RGD:1624291
G H3f3b H3 histone family member 3B JBrowse link 10 104,573,666 104,575,890 RGD:1624291

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 19858
    cellular process 18618
      cellular component organization or biogenesis 6706
        cellular component organization 6456
          chromatin organization 834
            chromatin organization involved in regulation of transcription 143
              chromatin organization involved in negative regulation of transcription 130
                chromatin silencing + 84
                heterochromatin assembly + 52
                heterochromatin organization involved in chromatin silencing + 7
Path 2
Term Annotations click to browse term
  biological_process 19858
    metabolic process 12097
      cellular metabolic process 10918
        cellular aromatic compound metabolic process 5567
          nucleobase-containing compound metabolic process 5344
            nucleic acid metabolic process 4850
              RNA metabolic process 4347
                regulation of RNA metabolic process 3510
                  negative regulation of RNA metabolic process 1418
                    negative regulation of RNA biosynthetic process 1316
                      negative regulation of nucleic acid-templated transcription 1314
                        negative regulation of transcription, DNA-templated 1280
                          chromatin organization involved in negative regulation of transcription 130
                            chromatin silencing + 84
                            heterochromatin assembly + 52
                            heterochromatin organization involved in chromatin silencing + 7
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.