PSENEN

presenilin enhancer, gamma-secretase subunit | PEN2

Presenilins, which are components of the gamma-secretase protein complex, are required for intramembranous processing of some type I transmembrane proteins, such as the Notch proteins and the beta-amyloid precursor protein. Signaling by Notch receptors mediates a wide range of developmental cell fates. Processing of the beta-amyloid precursor protein generates neurotoxic amyloid beta peptides, the major component of senile plaques associated with Alzheimer's disease. This gene encodes a protein that is required for Notch pathway signaling, and for the activity and accumulation of gamma-secretase. Mutations resulting in haploinsufficiency for this gene cause familial acne inversa-2 (ACNINV2). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

Member of: DE-1

Biological processes 45 terms

Golgi apparatus (GO:0005794)Golgi cisterna membrane (GO:0032580)Golgi membrane (GO:0000139)Notch receptor processing (GO:0007220)Notch receptor processing (GO:0007220)Notch receptor processing (GO:0007220)amyloid precursor protein catabolic process (GO:0042987)amyloid precursor protein catabolic process (GO:0042987)amyloid precursor protein catabolic process (GO:0042987)amyloid precursor protein catabolic process (GO:0042987)amyloid precursor protein metabolic process (GO:0042982)amyloid-beta formation (GO:0034205)amyloid-beta formation (GO:0034205)cellular response to glucose starvation (GO:0042149)cellular response to glucose starvation (GO:0042149)endopeptidase activator activity (GO:0061133)endopeptidase activator activity (GO:0061133)endopeptidase activator activity (GO:0061133)endoplasmic reticulum (GO:0005783)endoplasmic reticulum membrane (GO:0005789)endoplasmic reticulum membrane (GO:0005789)endosome membrane (GO:0010008)enzyme binding (GO:0019899)gamma-secretase complex (GO:0070765)gamma-secretase complex (GO:0070765)gamma-secretase complex (GO:0070765)gamma-secretase complex (GO:0070765)membrane (GO:0016020)membrane (GO:0016020)membrane protein ectodomain proteolysis (GO:0006509)membrane protein intracellular domain proteolysis (GO:0031293)molecular function inhibitor activity (GO:0140678)molecular function inhibitor activity (GO:0140678)negative regulation of TORC1 signaling (GO:1904262)negative regulation of TORC1 signaling (GO:1904262)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)positive regulation of endopeptidase activity (GO:0010950)presynaptic membrane (GO:0042734)protein binding (GO:0005515)protein processing (GO:0016485)protein processing (GO:0016485)protein processing (GO:0016485)protein processing (GO:0016485)

Expression (TPM)

TFs regulating PSENEN 0 TFs

Transcription factors with Perturb-seq knockdown data for PSENEN. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = PSENEN upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to PSENEN

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of PSENEN, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr19:35,471,034–35,471,539	274.3 kb	Distal (>10kb) Multiome	15
chr19:35,509,786–35,510,900	235.1 kb	Distal (>10kb) Multiome	650
chr19:35,545,067–35,546,126	200.0 kb	Distal (>10kb) Multiome	879
chr19:35,557,343–35,558,684	187.5 kb	Distal (>10kb) Multiome	452
chr19:35,612,546–35,613,176	132.9 kb	Distal (>10kb) Multiome	778
chr19:35,628,465–35,629,474	116.7 kb	Distal (>10kb) Multiome	889
chr19:35,641,602–35,642,192	103.8 kb	Distal (>10kb) Multiome	183
chr19:35,643,064–35,645,730	102.1 kb	Distal (>10kb) Multiome	1010
chr19:35,648,040–35,648,575	97.4 kb	Distal (>10kb) Multiome	599
chr19:35,673,179–35,673,643	72.2 kb	Distal (>10kb) Multiome	311
chr19:35,702,152–35,702,985	43.1 kb	Distal (>10kb) Multiome	662
chr19:35,716,025–35,718,811	27.9 kb	Distal (>10kb) Multiome	1018
chr19:35,740,083–35,741,430	4.8 kb	Proximal (<10kb) Multiome	829
chr19:35,744,481–35,746,086	314 bp	At TSS Multiome	679
chr19:35,748,170–35,749,017	2.9 kb	Proximal (<10kb) Multiome	749
chr19:35,757,432–35,758,657	12.5 kb	Distal (>10kb) Multiome	851
chr19:35,767,601–35,768,256	22.4 kb	Distal (>10kb) Multiome	276
chr19:35,775,066–35,776,063	29.9 kb	Distal (>10kb) Multiome	474
chr19:35,784,357–35,785,306	39.1 kb	Distal (>10kb) Multiome	183
chr19:35,860,621–35,861,651	115.7 kb	Distal (>10kb) Multiome	299
chr19:35,868,369–35,868,860	122.9 kb	Distal (>10kb) Multiome	320
chr19:35,869,343–35,870,482	124.3 kb	Distal (>10kb) Multiome	492
chr19:35,899,240–35,900,760	154.1 kb	Distal (>10kb) Multiome	751
chr19:35,931,342–35,932,167	186.1 kb	Distal (>10kb) Multiome	835
chr19:35,936,083–35,936,704	190.8 kb	Distal (>10kb) Multiome	417
chr19:35,986,945–35,987,622	241.7 kb	Distal (>10kb) Multiome	363
chr19:35,994,796–35,995,940	249.6 kb	Distal (>10kb) Multiome	897
chr19:36,008,519–36,009,006	263.2 kb	Distal (>10kb) Multiome	427
chr19:36,013,972–36,014,810	268.8 kb	Distal (>10kb) Multiome	623
chr19:36,032,424–36,033,187	287.3 kb	Distal (>10kb) Multiome	179

Genome Browser

Genomic view of the PSENEN locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.