NACC2

gene
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Also known as MGC23427BEND9BTBD31

Summary

NACC2 (NACC family member 2, HGNC:23846) is a protein-coding gene on chromosome 9q34.3, encoding Nucleus accumbens-associated protein 2 (Q96BF6). Functions as a transcriptional repressor through its association with the NuRD complex.

Enables several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; histone deacetylase binding activity; and protein homodimerization activity. Involved in several processes, including negative regulation of transcription by RNA polymerase II; positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage; and protein homooligomerization. Located in chromatin; mitochondrion; and nucleolus.

Source: NCBI Gene 138151 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 67 total
  • MANE Select transcript: NM_144653

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23846
Approved symbolNACC2
NameNACC family member 2
Location9q34.3
Locus typegene with protein product
StatusApproved
AliasesMGC23427, BEND9, BTBD31
Ensembl geneENSG00000148411
Ensembl biotypeprotein_coding
OMIM615786
Entrez138151

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000277554, ENST00000371753, ENST00000467669, ENST00000930481

RefSeq mRNA: 1 — MANE Select: NM_144653 NM_144653

CCDS: CCDS6993

Canonical transcript exons

ENST00000277554 — 6 exons

ExonStartEnd
ENSE00001352850136095189136095289
ENSE00003889367136013864136013969
ENSE00003890139136006537136012024
ENSE00003893831136013199136013296
ENSE00003893876136049636136050580
ENSE00003894415136016265136016429

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 99.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.4305 / max 69.0075, expressed in 1751 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1031176.80991687
1031181.90371219
1031161.71701091

Top tissues by expression

296 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
dorsal motor nucleus of vagus nerveUBERON:000287099.07gold quality
inferior olivary complexUBERON:000212798.76gold quality
medial globus pallidusUBERON:000247798.61gold quality
globus pallidusUBERON:000187598.37gold quality
lateral globus pallidusUBERON:000247697.93gold quality
endothelial cellCL:000011597.58gold quality
inferior vagus X ganglionUBERON:000536397.52gold quality
cranial nerve IIUBERON:000094197.48gold quality
lateral nuclear group of thalamusUBERON:000273697.31gold quality
medulla oblongataUBERON:000189696.92gold quality
choroid plexus epitheliumUBERON:000391196.92gold quality
substantia nigra pars reticulataUBERON:000196696.81gold quality
subthalamic nucleusUBERON:000190696.79gold quality
substantia nigra pars compactaUBERON:000196596.67gold quality
postcentral gyrusUBERON:000258196.38gold quality
CA1 field of hippocampusUBERON:000388196.31gold quality
superior vestibular nucleusUBERON:000722796.12gold quality
dorsal plus ventral thalamusUBERON:000189795.94gold quality
parietal lobeUBERON:000187295.66gold quality
entorhinal cortexUBERON:000272895.57gold quality
spinal cordUBERON:000224095.56gold quality
C1 segment of cervical spinal cordUBERON:000646995.50gold quality
ponsUBERON:000098895.49gold quality
blood vessel layerUBERON:000479795.47gold quality
seminal vesicleUBERON:000099895.36gold quality
saphenous veinUBERON:000731895.17gold quality
ventral tegmental areaUBERON:000269195.16gold quality
temporal lobeUBERON:000187194.47gold quality
midbrainUBERON:000189194.47gold quality
amygdalaUBERON:000187694.35gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.94
E-MTAB-6142no43.96

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
MDM2Repression

JASPAR motifs

MotifNameFamily
MA2507.1NACC2Other factors with up to three adjacent zinc fingers
MA2559.1NACC2Other factors with up to three adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:35144965

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

228 targeting NACC2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-8485100.0077.574731
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4476100.0068.182030
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-4692100.0067.322066
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-5193100.0067.261744
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4262100.0073.263931
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-6798-5P100.0065.77699
HSA-MIR-4533100.0069.482758
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-3120-5P100.0065.56965
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-451499.9967.101870
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997

Literature-anchored findings (GeneRIF, showing 2)

  • RBB is a novel transcriptional repressor and an important regulator of p53 pathway. (PMID:22926524)
  • NACC2, a molecular effector of miR-132 regulation at the interface between adult neurogenesis and Alzheimer’s disease. (PMID:39256511)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusNacc2ENSMUSG00000026932
rattus_norvegicusNacc2ENSRNOG00000018231

Paralogs (28): ZNF280C (ENSG00000056277), ZBTB25 (ENSG00000089775), PRDM13 (ENSG00000112238), BCL6 (ENSG00000113916), FEZF1 (ENSG00000128610), ZBTB46 (ENSG00000130584), PRDM12 (ENSG00000130711), ZNF280D (ENSG00000137871), FEZF2 (ENSG00000153266), ZBTB7B (ENSG00000160685), NACC1 (ENSG00000160877), BCL6B (ENSG00000161940), GFI1 (ENSG00000162676), GFI1B (ENSG00000165702), ZBTB49 (ENSG00000168826), ZNF280A (ENSG00000169548), ZNF581 (ENSG00000171425), ZNF524 (ENSG00000171443), ZBTB26 (ENSG00000171448), ZBTB21 (ENSG00000173276), ZNF683 (ENSG00000176083), ZBTB33 (ENSG00000177485), ZBTB3 (ENSG00000185670), ZBTB6 (ENSG00000186130), ZBTB14 (ENSG00000198081), ZBTB12 (ENSG00000204366), ZNF580 (ENSG00000213015), ZNF280B (ENSG00000275004)

Protein

Protein identifiers

Nucleus accumbens-associated protein 2Q96BF6 (reviewed: Q96BF6)

Alternative names: BTB/POZ domain-containing protein 14A, Repressor with BTB domain and BEN domain

All UniProt accessions (1): Q96BF6

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a transcriptional repressor through its association with the NuRD complex. Recruits the NuRD complex to the promoter of MDM2, leading to the repression of MDM2 transcription and subsequent stability of p53/TP53.

Subunit / interactions. Homooligomer; mediated by the BTB domain. Interacts with the NuRD complex. Interacts (via C-terminal part) with HDAC2. Interacts (via BTB domain) with MTA1, MTA2 and MTA3.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_653254* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily
IPR018379BEN_domainDomain
IPR050457ZnFinger_BTB_dom_containFamily

Pfam: PF00651, PF10523

UniProt features (12 total): cross-link 5, domain 2, region of interest 2, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96BF6-F161.410.27

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (5): 429, 456, 174, 217, 299

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 241 (showing top): GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, TGACCTY_ERR1_Q2, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, ONKEN_UVEAL_MELANOMA_UP, GOBP_APOPTOTIC_SIGNALING_PATHWAY, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_RESPONSE_TO_DNA_DAMAGE, GOBP_DNA_DAMAGE_RESPONSE, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, GOBP_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_REGULATION_OF_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_RESPONSE_TO_DNA_DAMAGE, GOBP_PROTEIN_HOMOOLIGOMERIZATION

GO Biological Process (8): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of cell population proliferation (GO:0008285), protein-containing complex localization (GO:0031503), negative regulation of DNA-templated transcription (GO:0045892), protein homooligomerization (GO:0051260), positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231), regulation of cell population proliferation (GO:0042127)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), protein homodimerization activity (GO:0042803), histone deacetylase binding (GO:0042826), protein-containing complex binding (GO:0044877), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), nucleolus (GO:0005730), mitochondrion (GO:0005739), nuclear lumen (GO:0031981)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
regulation of transcription by RNA polymerase II2
transcription by RNA polymerase II2
regulation of DNA-templated transcription2
cell population proliferation2
binding2
intracellular membrane-bounded organelle2
negative regulation of DNA-templated transcription1
regulation of cell population proliferation1
negative regulation of cellular process1
macromolecule localization1
DNA-templated transcription1
negative regulation of RNA biosynthetic process1
protein complex oligomerization1
intrinsic apoptotic signaling pathway in response to DNA damage1
regulation of intrinsic apoptotic signaling pathway in response to DNA damage1
positive regulation of intrinsic apoptotic signaling pathway1
regulation of cellular process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
identical protein binding1
protein dimerization activity1
enzyme binding1
nucleic acid binding1
chromosome1
cellular anatomical structure1
nuclear lumen1
intracellular membraneless organelle1
cytoplasm1
nucleus1
intracellular organelle lumen1

Protein interactions and networks

STRING

788 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NACC2PPP1R26Q5T8A7511
NACC2HINFPQ9BQA5497
NACC2ETV6P41212474
NACC2BEND3Q5T5X7463
NACC2QKIQ96PU8444
NACC2BEND6Q5SZJ8431
NACC2RB1CC1Q8TDY2428
NACC2RBL2Q08999428
NACC2RB1P06400416
NACC2MORC3Q14149408
NACC2TRIM27P14373401
NACC2ID2Q02363390
NACC2DGCR8Q8WYQ5389
NACC2BTBD1Q9H0C5379
NACC2GPR37L1O60883379
NACC2BEND7Q8N7W2379

IntAct

34 interactions, top by confidence:

ABTypeScore
RFXANKRFXAPpsi-mi:“MI:0914”(association)0.780
VHLNACC2psi-mi:“MI:0915”(physical association)0.560
FOXP3FOXP2psi-mi:“MI:0914”(association)0.530
HSPB8VWA8psi-mi:“MI:0914”(association)0.530
DNAJB8DNAJB6psi-mi:“MI:0914”(association)0.530
RPP21POP7psi-mi:“MI:0914”(association)0.530
EPS8NACC2psi-mi:“MI:0915”(physical association)0.370
ZBTB34CHEK1psi-mi:“MI:0914”(association)0.350
BCANHSPA5psi-mi:“MI:0914”(association)0.350
NACC2FHL2psi-mi:“MI:0914”(association)0.350
B4GALT2LENG9psi-mi:“MI:0914”(association)0.350
BORCS8SH3PXD2Bpsi-mi:“MI:0914”(association)0.350
NPAS1CIBAR1psi-mi:“MI:0914”(association)0.350
INF2PIPSLpsi-mi:“MI:0914”(association)0.350
SENP3IPO5psi-mi:“MI:0914”(association)0.350
TPGS1PIK3R2psi-mi:“MI:0914”(association)0.350
PPARDACACBpsi-mi:“MI:0914”(association)0.350
C6orf141ZNF195psi-mi:“MI:0914”(association)0.350
DNAJB6SCAMP1psi-mi:“MI:0914”(association)0.350
DHDHZNF185psi-mi:“MI:0914”(association)0.350
NCAPH2FANCApsi-mi:“MI:0914”(association)0.350
SOHLH1FANCApsi-mi:“MI:0914”(association)0.350
TFPTCCP110psi-mi:“MI:0914”(association)0.350
DCTN3RPS6KA4psi-mi:“MI:0914”(association)0.350
AANATUBBpsi-mi:“MI:0914”(association)0.350
TWIST2TCF3psi-mi:“MI:0914”(association)0.350
CIB3PCK1psi-mi:“MI:0914”(association)0.350
C11orf71MNAT1psi-mi:“MI:0914”(association)0.350

BioGRID (61): NACC2 (Affinity Capture-MS), NACC2 (Affinity Capture-RNA), NACC2 (Affinity Capture-RNA), NACC2 (Positive Genetic), NACC1 (Affinity Capture-MS), NACC2 (Affinity Capture-MS), NACC2 (Affinity Capture-MS), OSBPL1A (Affinity Capture-MS), FHL2 (Affinity Capture-MS), GOPC (Affinity Capture-MS), FEM1A (Affinity Capture-MS), TRAPPC9 (Affinity Capture-MS), NACC2 (Affinity Capture-MS), NACC2 (Affinity Capture-MS), NACC2 (Affinity Capture-MS)

ESM2 similar proteins: A6QPM3, A7X8B3, A7X8B5, A7X8B7, A7X8B9, A7X8C2, A7X8C4, A7X8C7, A7X8C9, A7X8D2, A7X8D4, A7XW16, A7XW20, A7XW25, E9Q3T6, E9Q6W4, J7FCF0, O14512, O42406, O70361, O75626, O95863, O97775, O97952, O97960, P06186, P06401, P07812, P10275, P41182, P41183, Q02085, Q0VDT2, Q3UZD5, Q562B4, Q5IS79, Q5U5Q3, Q60688, Q62233, Q6F2E4

Diamond homologs: A0JN76, A1L2U9, A1YPR0, B1WAZ8, B1WBS3, B1WBU4, B2RXF5, E1B932, G5E8B9, O14867, O15062, O43167, O43298, O88282, O88939, O93567, O95365, O95625, P10074, P28575, P41182, P41183, P52739, P97302, P97303, Q0IH98, Q0IJ29, Q0P4X6, Q0VCJ6, Q13105, Q14526, Q1H9T6, Q1L8W0, Q3B725, Q3B7M1, Q3B7N9, Q3SWU4, Q3ZB90, Q503R4, Q53G59

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

67 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance54
Likely benign4
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1940 predictions. Top by Δscore:

VariantEffectΔscore
9:136011658:T:TAdonor_gain1.0000
9:136012023:CA:Cacceptor_gain1.0000
9:136012025:C:CCacceptor_gain1.0000
9:136013194:CTTAC:Cdonor_loss1.0000
9:136013196:TAC:Tdonor_loss1.0000
9:136013197:A:ACdonor_gain1.0000
9:136013197:ACA:Adonor_loss1.0000
9:136013198:C:CAdonor_gain1.0000
9:136013198:CA:Cdonor_gain1.0000
9:136013198:CAT:Cdonor_gain1.0000
9:136013198:CATT:Cdonor_gain1.0000
9:136013198:CATTT:Cdonor_gain1.0000
9:136013292:TGTTC:Tacceptor_gain1.0000
9:136013294:TTC:Tacceptor_gain1.0000
9:136013295:TC:Tacceptor_gain1.0000
9:136013296:CC:Cacceptor_gain1.0000
9:136013297:C:CCacceptor_gain1.0000
9:136013297:CTG:Cacceptor_loss1.0000
9:136013300:G:Cacceptor_gain1.0000
9:136013300:G:GCacceptor_gain1.0000
9:136013310:C:CTacceptor_gain1.0000
9:136013310:C:Tacceptor_gain1.0000
9:136013311:G:Tacceptor_gain1.0000
9:136016260:CTCA:Cdonor_loss1.0000
9:136016262:CAC:Cdonor_loss1.0000
9:136016264:C:CTdonor_loss1.0000
9:136016266:TGCC:Tdonor_gain1.0000
9:136016428:CA:Cacceptor_gain1.0000
9:136049630:CGTTA:Cdonor_loss1.0000
9:136049631:GTTAC:Gdonor_loss1.0000

AlphaMissense

3812 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:136011927:C:AW451C1.000
9:136011927:C:GW451C1.000
9:136011929:A:GW451R1.000
9:136011929:A:TW451R1.000
9:136011943:C:GR446P1.000
9:136011944:G:TR446S1.000
9:136011946:C:GR445P1.000
9:136011947:G:TR445S1.000
9:136011949:G:TA444D1.000
9:136011951:G:CN443K1.000
9:136011951:G:TN443K1.000
9:136011952:T:AN443I1.000
9:136011953:T:CN443D1.000
9:136011955:G:AT442I1.000
9:136011957:G:CC441W1.000
9:136011958:C:AC441F1.000
9:136011958:C:GC441S1.000
9:136011958:C:TC441Y1.000
9:136011959:A:GC441R1.000
9:136011959:A:TC441S1.000
9:136011960:C:AM440I1.000
9:136011960:C:GM440I1.000
9:136011960:C:TM440I1.000
9:136011961:A:CM440R1.000
9:136011961:A:GM440T1.000
9:136011961:A:TM440K1.000
9:136011963:G:CD439E1.000
9:136011963:G:TD439E1.000
9:136011964:T:AD439V1.000
9:136011964:T:CD439G1.000

dbSNP variants (sampled 300 via entrez): RS1000031585 (9:136041058 G>A), RS1000087747 (9:136070164 G>T), RS1000097752 (9:136021135 G>A,C), RS1000154102 (9:136056199 C>T), RS1000214021 (9:136058625 G>A,C), RS1000226889 (9:136086693 C>A), RS1000234340 (9:136020363 G>A), RS1000239619 (9:136060211 T>C), RS1000278031 (9:136096078 C>T), RS1000281676 (9:136082586 C>T), RS1000283833 (9:136051659 G>A), RS1000328751 (9:136070033 A>C), RS1000332775 (9:136030334 G>A), RS1000333882 (9:136091082 T>C), RS1000359894 (9:136090459 G>A)

Disease associations

OMIM: gene MIM:615786 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

StudyTraitp-value
GCST004131_21Inflammatory bowel disease5.000000e-36
GCST004132_11Crohn’s disease6.000000e-30
GCST004133_17Ulcerative colitis2.000000e-16
GCST012796_7Sjögren’s syndrome5.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

55 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
methylmercuric chlorideincreases expression, affects cotreatment3
Benzo(a)pyreneincreases expression, affects methylation, decreases methylation3
Valproic Acidincreases methylation, decreases expression, increases expression3
bisphenol Aaffects cotreatment, affects methylation, decreases methylation, increases expression2
entinostatincreases expression, affects cotreatment2
Acetaminophendecreases expression2
Air Pollutantsaffects cotreatment, decreases expression, increases abundance, affects expression2
Ozoneaffects expression, affects cotreatment, decreases expression, increases abundance2
bisphenol Faffects cotreatment, increases expression1
TAK-243increases sumoylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
propionaldehydeincreases expression1
pirinixic acidaffects binding, decreases expression, increases activity1
testosterone undecanoateaffects cotreatment, decreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydeincreases expression1
aflatoxin B2decreases methylation1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
cylindrospermopsinincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
PCI 5002affects cotreatment, increases expression1
Temozolomideincreases expression1
Sunitinibdecreases expression1
Fulvestrantaffects cotreatment, affects methylation1
Leflunomidedecreases expression1
Acroleinaffects cotreatment, decreases expression, increases abundance1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Sjogren syndrome