uu.seUppsala universitets publikasjoner
Endre søk
RefereraExporteraLink to record
Permanent link

Direct link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.
Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Larhammar: Farmakologi.
Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.ORCID-id: 0000-0001-9460-390x
Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Medicinsk genetik och genomik. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
Vise andre og tillknytning
2019 (engelsk)Inngår i: BMC Biotechnology, ISSN 1472-6750, E-ISSN 1472-6750, Vol. 19, artikkel-id 31Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Background: Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome.

Results: We have investigated 18 individuals from the 1000 Genomes project using the well-established method of read depth analysis and the new droplet digital PCR (ddPCR) method. We find that the most common copy number for NPY4R is 4. The estimated number of copies ranged from three to seven based on read depth analyses with Control-FREEC and CNVnator, and from four to seven based on ddPCR. We suggest that the difference between our results and those published previously can be explained by methodological differences such as reference gene choice, data normalization and method reliability. Three high-quality archaic human genomes (two Neanderthal and one Denisova) display four copies of the NPY4R gene indicating that a duplication occurred prior to the human-Neanderthal/Denisova split.

Conclusions: We conclude that ddPCR is a sensitive and reliable method for CNV determination, that it can be used for read depth calibration in CNV studies based on already available whole-genome sequencing data, and that further investigation of NPY4R copy number variation and its consequences are necessary due to the role of Y4 receptor in food intake regulation.

sted, utgiver, år, opplag, sider
2019. Vol. 19, artikkel-id 31
HSV kategori
Identifikatorer
URN: urn:nbn:se:uu:diva-356569DOI: 10.1186/s12896-019-0523-9ISI: 000470281900001PubMedID: 31164119OAI: oai:DiVA.org:uu-356569DiVA, id: diva2:1236206
Forskningsfinansiär
Swedish Research CouncilThe Swedish Brain FoundationTilgjengelig fra: 2018-08-01 Laget: 2018-08-01 Sist oppdatert: 2019-06-25bibliografisk kontrollert
Inngår i avhandling
1. The human pancreatic polypeptide receptor Y4: Genetic and functional variation
Åpne denne publikasjonen i ny fane eller vindu >>The human pancreatic polypeptide receptor Y4: Genetic and functional variation
2018 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
Abstract [en]

Humans are evolutionarily adapted to an environment where food is scarce, but today many live in a world of food abundance. Paired with low physical activity, this may lead to weight gain and obesity. Efficient anti-obesity treatments require understanding of the mechanisms that control hunger, satiety, energy metabolism and body weight. This thesis investigates possible genetic and physiological mechanisms behind these processes.

Genetic correlation between body-mass index (BMI) and a highly polymorphic region on chromosome 10 was analysed with regard to single nucleotide polymorphisms (SNPs) and gene copy number variation (CNV). This region contains the gene NPY4R encoding the pancreatic polypeptide (PP) receptor Y4, which has been reported to reduce appetite.

The results show that the NPY4R gene was duplicated before the divergence of modern humans from the Neanderthals and the Denisovans (approximately to 400,000–800,000 years ago). The CNV of the NPY4R gene region was investigated by read depth analysis based on genome sequences and droplet digital PCR (ddPCR). The read depth results revealed a CNV range of 3-7 copies per genome, while the ddPCR results demonstrated a range of 2–11. Most humans have a total of 4–5 copies, in contrast to the two copies presumed by previous studies.

Investigation of an association between the NPY4R CNV and body mass index (BMI) led to interesting and ambiguous results. A study of 558 Swedish individuals with a wide range of BMI suggested, surprisingly, a positive correlation between NPY4R copy number and BMI for women. On the other hand, a study of 1009 individuals from Northern Sweden found no correlation between BMI and NPY4R copy number. These diverging findings may be due to geographical variation or lack of power in one of these studies.

Twelve naturally-occurring amino acid variants of the Y4 receptor were investigated pharmacologically in cell culture. Three of these showed no functional response, which may be explained by altered conformation of the receptors. For two receptor variants PP had a significantly decreased potency. A 3D model of the Y4 receptor was generated based on the crystal structure of the human Y1 receptor. The functional responses of the Y4 variants agree well with the 3D model and with the degree of evolutionary conservation of the positions.

In conclusion, these studies reveal unexpectedly large CNV as well as extensive SNP for the NPY4R gene and a possible correlation with BMI that may be due to the differing responses of the naturally occurring receptor variants.

sted, utgiver, år, opplag, sider
Uppsala: Acta Universitatis Upsaliensis, 2018. s. 53
Serie
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1479
Emneord
NPY4R, Y4, obesity, CNV
HSV kategori
Forskningsprogram
Medicinsk vetenskap
Identifikatorer
urn:nbn:se:uu:diva-356573 (URN)978-91-513-0389-5 (ISBN)
Disputas
2018-09-18, C2:301, BMC, Husargatan 3, Uppsala, 09:15 (engelsk)
Opponent
Veileder
Tilgjengelig fra: 2018-08-24 Laget: 2018-08-01 Sist oppdatert: 2018-09-07

Open Access i DiVA

fulltext(821 kB)29 nedlastinger
Filinformasjon
Fil FULLTEXT01.pdfFilstørrelse 821 kBChecksum SHA-512
234d218ed2495e8144633a6b9e12b4a79370744c36d55eaae073921304efb3f91c4299c71ad15699634e45c4d973dc36a3f64a793bc25360ba488fe794c3af43
Type fulltextMimetype application/pdf

Andre lenker

Forlagets fulltekstPubMed

Personposter BETA

Shebanits, KaterynaGünther, TorstenJohansson, Anna C. V.Maqbool, KhurramFeuk, LarsJakobsson, MattiasLarhammar, Dan

Søk i DiVA

Av forfatter/redaktør
Shebanits, KaterynaGünther, TorstenJohansson, Anna C. V.Maqbool, KhurramFeuk, LarsJakobsson, MattiasLarhammar, Dan
Av organisasjonen
I samme tidsskrift
BMC Biotechnology

Søk utenfor DiVA

GoogleGoogle Scholar
Totalt: 29 nedlastinger
Antall nedlastinger er summen av alle nedlastinger av alle fulltekster. Det kan for eksempel være tidligere versjoner som er ikke lenger tilgjengelige

doi
pubmed
urn-nbn

Altmetric

doi
pubmed
urn-nbn
Totalt: 781 treff
RefereraExporteraLink to record
Permanent link

Direct link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf