Suomalaisten Y-kromosomaalisten haploryhmien määrittäminen genotyyppisirudatasta : kohti ymmärrystä Y-kromosomin roolista monitekijäisissä sairauksissa

Y-kromosomilla on olennainen rooli ihmisen ja muiden nisäkkäiden geneettisessä sukupuolenmäärityksessä. Se sisältää miehille ominaisen MSY-alueen, joka ei rekombinoi, ja siten periytyy yksinomaan miesten sukulinjan kautta. MSY-alueen geneettiset variaatiot periytyvät yhdessä ja siten Y-kromosomit voidaan lajitella haploryhmiin. Y-kromosomaaliset haploryhmät sisältävät informaatiota geneettisestä alkuperästä, joten Y-kromosomeja on käytetty laajalti ihmisen historian jäljittämisessä. Y-kromosomille ominaiset biologiset ja analyyttiset haasteet huomioon ottaen Y-kromosomi jätetään usein rutiininomaisesti pois geneettisistä assosiaatiotutkimuksista. Näin ollen Y-kromosomaalisen geneettisen vaihtelun mahdolliset vaikutukset monitekijäisissä sairauksissa ovat suurelta osin määritelmättä. Viime aikoina Y-kromosomin geneettisten assosiaatiotutkimusten laajentaminen on ollut mahdollista laajamittaisten biopankkidatojen avulla. Äskettäisessä Ison-Britannian biopankkitutkimuksessa ehdotettiin assosiaatiota Y-kromosomaalisen I1-haploryhmän ja sepelvaltimotaudin (CAD) välillä Ison-Britannian väestössä, mutta tätä tulosta ei ole vahvistettu muissa aineistoissa. Koska I1-haploryhmä on yleinen Suomen väestössä, voidaan tätä I1-haploryhmän ja sepelvaltimotaudin välistä yhteyttä tutkia FinnGen-projektin datan avulla. Tämän tutkielman ensimmäisenä tavoitteena oli selvittää Y-kromosomaalisten haploryhmien yleisyys Suomessa, ja luonnehtia haploryhmien maantieteellistä jakautumista Suomessa käyttämällä FinnGen-projektin genotyyppisirudataa. Toisena tavoitteena oli tutkia suomalaisten Y-kromosomaalisten haploryhmien ja sepelvaltimotaudin (CAD) välistä yhteyttä logistisella regressioanalyysillä. Tämä tutkielma määritteli Y-kromosomaalisia haploryhmiä Suomessa 24 160 miehelle ja tutki näiden Y-kromosomaalisten haploryhmien ja sepelvaltimotaudin välistä yhteyttä. Tutkimuksen aineisto oli moninkertainen aiempiin tutkimuksiin verrattuna, tarjoten mahdollisuuden tutkia Y-kromosomaalisen variaation maantieteellistä jakaumaa Suomessa ja tämän merkitystä monitekijäisille taudeille huomattavasti aiempia tutkimuksia tarkemmin. Y-kromosomaalisten haploryhmien maantieteellinen jakauma karakterisoitiin sekä 20 syntymäalueella että Suomen itä- ja länsiosien välillä. Aikaisempien tutkimusten mukaisesti tulokset osoittivat, että kahden yleisen suomalaisen Y-kromosomaalisten N1c1- ja I1-haploryhmien välillä ilmeni eroja esiintyvyydessä alueellisesti, etenkin Itä- ja Länsi-Suomen välillä. Tulokset logistisista regressioanalyyseistä sepelvaltimotaudin ja Y-kromosomaalisten haploryhmien välillä eivät osoittaneet merkitsevää yhteyttä I1 haploryhmän ja sepelvaltimoataudin välillä. Sen sijaan yleisimmällä suomalaisella Y-kromosomaalisella N1c1-haploryhmällä oli vähentynyt riski sepelvaltimotaudille assosiaatioanalyysissä verrattuna muihin haploryhmiin. Tulokset osoittivat myös, että Y-kromosomaalisten haploryhmien assosiaatiotulokset eivät olleet suoraan vertailukelpoisia populaatioiden välillä. Esimerkiksi sepelvaltimotaudin ja Y-kromosomaalisen I1-haploryhmän välinen assosiaatio osoitti alentuneen sepelvaltimotautiriskin verrattaessa R1b-haploryhmään FinnGen aineistossa, kun taas saman assosiaation ilmoitettiin lisäävän sepelvaltimotauti-riskiä Isossa-Britanniassa. Kaiken kaikkiaan tämä tutkielma osoittaa mahdollisuuden tutkia Y-kromosomien genetiikkaa FinnGen-projektin datan avulla ja korostaa tämän genomin osan sisällyttämisen arvoa tulevissa monitekijäisten sairauksien tutkimuksissa.The Y chromosome has an essential role in the genetic sex determination in humans and other mammals. It contains a male-specific region (MSY) which escapes recombination and is inherited exclusively through the male line. The genetic variations inherited together on the MSY can be used in classifying Y chromosomes into haplogroups. Y-chromosomal haplogroups are highly informative of genetic ancestry, thus Y chromosomes have been widely used in tracing human population history. However, given the peculiar biology and analytical challenges specific to the Y chromosome, the chromosome is routinely excluded from genetic association studies. Consequently, potential impacts of Y-chromosomal variation on complex disease remain largely uncharacterized. Lately the access to large-scale biobank data has enabled to extend the Y-chromosomal genetic association studies. A recent UK Biobank study suggested links between Y-chromosomal haplogroup I1 and coronary artery disease (CAD) in the British population, but this result has not been validated in other datasets. Since Finland harbours a notable frequency of Y-chromosomal haplogroup I1, the relationship between haplogroup I1 and CAD can further be inferred in the Finnish population using data from the FinnGen project. The first aim of this thesis was to determine the prevalence of Y-chromosomal haplogroups in Finland and characterize their geographical distributions using genotyping array data from the FinnGen project. The second aim was to assess the role between Finnish Y-chromosomal haplogroups and coronary artery disease (CAD) by logistic regression. This thesis characterized the Y-chromosomal haplogroups in Finland for 24 160 males and evaluated the association between Y-chromosomal haplogroups and CAD in Finland. The dataset used in this study was extensive, providing an opportunity to study the Y-chromosomal variation geographically in Finland and its role in complex disease more accurately compared to previous studies. The geographical distribution of the Y-chromosomal haplogroups was characterized on 20 birth regions, and between eastern and western areas of Finland. Consistent with previous studies, the results demonstrated that two major Finnish Y-chromosomal haplogroup lineages, N1c1 and I1, displayed differing distributions within regions, especially between eastern and western Finland. Results from logistic regression analysis between CAD and Y-chromosomal haplogroups suggested no significant association between haplogroup I1 and CAD. Instead, the major Finnish Y-chromosomal haplogroup N1c1 displayed a decreased risk for CAD in the association analysis when compared against other haplogroups. Moreover, this thesis also demonstrated that the association results were not straightforwardly comparable between populations. For instance, haplogroup I1 displayed a decreased risk for CAD in the FinnGen dataset when compared against haplogroup R1b, whereas the same association was reported as risk increasing for CAD in the UK Biobank. Overall, this thesis demonstrates the possibility to study the genetics of Y chromosome using data from the FinnGen project, and highlights the value of including this part of the genome in the future complex disease studies

Tageszeitabhängige Körpertemperaturrhythmen regulieren die Genexpression

Das alternative Spleißen ist ein dynamisch regulierter Mechanismus, der die Kodierungskapazität drastisch erhöht. Das alternative Spleißen ist in Tageszeitabhängig geregelt und hängt von Säugetierkörpertemperaturzyklen ab. Diese Beobachtung führte zu der Entdeckung einer körpertemperaturempfindlichen Kinase, die als Sensor wirkt, der kleine Temperaturänderungen (~ 1 ° C) in eine veränderte Phosphorylierung von RNA-Bindungsproteinen übersetzt, die wiederum über 1,500 Spleißereignisse steuern.Alternative splicing is a dynamically regulated mechanism that dramatically increases the genomes coding capacity. Alternative splicing is regulated in a time-of-day dependent manner and depends on mammalian body temperature cycles. This observation let to the discovery of a body temperature sensitive kinase, which acts as sensor translating small changes in temperature (∼ 1 °C) into altered phosphorylation of RNA-binding proteins, which in turn control over 1.500 splicing events

Customized eye models for determining optimized intraocular lenses power

We have developed a new optical procedure to determine the optimum power of intraocular lenses (IOLs) for cataract surgery. The procedure is based on personalized eye models, where biometric data of anterior corneal shape and eye axial length are used. A polychromatic exact ray-tracing through the surfaces defining the eye model is performed for each possible IOL power and the area under the radial MTF is used as a metric. The IOL power chosen by the procedure maximizes this parameter. The IOL power for 19 normal eyes has been determined and compared with standard regression-based predictions. The impact of the anterior corneal monochromatic aberrations and the eye’s chromatic aberration on the power predictions has been studied, being significant for those eyes with severe monochromatic aberrations, such as post-LASIK cataract patients, and for specific IOLs with low Abbe numbers

Sec16 alternative splicing dynamically controls COPII transport efficiency

The transport of secretory proteins from the endoplasmic reticulum (ER) to the Golgi depends on COPII-coated vesicles. While the basic principles of the COPII machinery have been identified, it remains largely unknown how COPII transport is regulated to accommodate tissue- or activation-specific differences in cargo load and identity. Here we show that activation-induced alternative splicing of Sec16 controls adaptation of COPII transport to increased secretory cargo upon T-cell activation. Using splice-site blocking morpholinos and CRISPR/Cas9-mediated genome engineering, we show that the number of ER exit sites, COPII dynamics and transport efficiency depend on Sec16 alternative splicing. As the mechanistic basis, we suggest the C-terminal Sec16 domain to be a splicing-controlled protein interaction platform, with individual isoforms showing differential abilities to recruit COPII components. Our work connects the COPII pathway with alternative splicing, adding a new regulatory layer to protein secretion and its adaptation to changing cellular environments

Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8

Small nuclear ribonucleoprotein complexes (snRNPs) represent the main subunits of the spliceosome. While the assembly of the snRNP core particles has been well characterized, comparably little is known of the incorporation of snRNP-specific proteins and the mechanisms of snRNP recycling. U5 snRNP assembly in yeast requires binding of the the Aar2 protein to Prp8p as a placeholder to preclude premature assembly of the SNRNP200 helicase, but the role of the human AAR2 homolog has not yet been investigated in detail. Here, a crystal structure of human AAR2 in complex with the RNase H-like domain of the U5-specific PRPF8 (PRP8F RH) is reported, revealing a significantly different interaction between the two proteins compared with that in yeast. Based on the structure of the AAR2–PRPF8 RH complex, the importance of the interacting regions and residues was probed and AAR2 variants were designed that failed to stably bind PRPF8 in vitro. Protein-interaction studies of AAR2 with U5 proteins using size-exclusion chromatography reveal similarities and marked differences in the interaction patterns compared with yeast Aar2p and imply phosphorylation-dependent regulation of AAR2 reminiscent of that in yeast. It is found that in vitro AAR2 seems to lock PRPF8 RH in a conformation that is only compatible with the first transesterification step of the splicing reaction and blocks a conformational switch to the step 2-like, Mg2+-coordinated conformation that is likely during U5 snRNP biogenesis. These findings extend the picture of AAR2 PRP8 interaction from yeast to humans and indicate a function for AAR2 in the spliceosomal assembly process beyond its role as an SNRNP200 placeholder in yeast

A Snu114-GTP-Prp8 module forms a relay station for efficient splicing in yeast

The single G protein of the spliceosome, Snu114, has been proposed to facilitate splicing as a molecular motor or as a regulatory G protein. However, available structures of spliceosomal complexes show Snu114 in the same GTP-bound state, and presently no Snu114 GTPase-regulatory protein is known. We determined a crystal structure of Snu114 with a Snu114-binding region of the Prp8 protein, in which Snu114 again adopts the same GTP-bound conformation seen in spliceosomes. Snu114 and the Snu114-Prp8 complex co-purified with endogenous GTP. Snu114 exhibited weak, intrinsic GTPase activity that was abolished by the Prp8 Snu114-binding region. Exchange of GTP-contacting residues in Snu114, or of Prp8 residues lining the Snu114 GTP-binding pocket, led to temperature-sensitive yeast growth and affected the same set of splicing events in vivo. Consistent with dynamic Snu114-mediated protein interactions during splicing, our results suggest that the Snu114-GTP-Prp8 module serves as a relay station during spliceosome activation and disassembly, but that GTPase activity may be dispensable for splicing

Idaho Completion Project’s Accelerated Retrieval Project Overview of the Pit 4 Non-Time Critical Removal Action

This paper presents an overview of the Accelerated Retrieval Project performed by the Idaho Completion Project at the Idaho National Laboratory (INL). Topics include an overall description of the process and methods that will retrieve, characterize, and certify newly generated transuranic (TRU) waste for disposal at the Waste Isolation Pilot Plant (WIPP). The retrieval and characterization of buried TRU waste presents unique challenges. Innovative approaches developed and discussed are: excavation, RCRA waste sampling, visual examination, and deployment of the WIPP Central Characterization Project mobile systems to the INL

Splicing-accessible coding 3′UTRs control protein stability and interaction networks

Background 3′-Untranslated regions (3′UTRs) play crucial roles in mRNA metabolism, such as by controlling mRNA stability, translation efficiency, and localization. Intriguingly, in some genes the 3′UTR is longer than their coding regions, pointing to additional, unknown functions. Here, we describe a protein-coding function of 3′UTRs upon frameshift-inducing alternative splicing in more than 10% of human and mouse protein-coding genes. Results 3′UTR-encoded amino acid sequences show an enrichment of PxxP motifs and lead to interactome rewiring. Furthermore, an elevated proline content increases protein disorder and reduces protein stability, thus allowing splicing-controlled regulation of protein half-life. This could also act as a surveillance mechanism for erroneous skipping of penultimate exons resulting in transcripts that escape nonsense mediated decay. The impact of frameshift-inducing alternative splicing on disease development is emphasized by a retinitis pigmentosa-causing mutation leading to translation of a 3′UTR-encoded, proline-rich, destabilized frameshift-protein with altered protein-protein interactions. Conclusions We describe a widespread, evolutionarily conserved mechanism that enriches the mammalian proteome, controls protein expression and protein-protein interactions, and has important implications for the discovery of novel, potentially disease-relevant protein variants

Feasibility Study for Operable Unit 7-13/14

The Subsurface Disposal Area is a radioactive waste landfill located within the Radioactive Waste Management Complex at the Idaho National Laboratory Site in southeastern Idaho. This Feasibility Study for Operable Unit 7-13/14 analyzes options for mitigating risks to human health and the environment associated with the landfill. Analysis is conducted in accordance with the Comprehensive Environmental Response, Compensation, and Liability Act, using nine evaluation criteria to develop detailed and comparative analysis of five assembled alternatives. Assembled alternatives are composed of discrete modules. Ultimately, decision-makers will select, recombine, and sum various modules into an optimized preferred alternative and final remedial decision

Regulation of 3′ splice site selection after step 1 of splicing by spliceosomal C* proteins

Alternative precursor messenger RNA splicing is instrumental in expanding the proteome of higher eukaryotes, and changes in 3′ splice site (3'ss) usage contribute to human disease. We demonstrate by small interfering RNA–mediated knockdowns, followed by RNA sequencing, that many proteins first recruited to human C* spliceosomes, which catalyze step 2 of splicing, regulate alternative splicing, including the selection of alternatively spliced NAGNAG 3′ss. Cryo–electron microscopy and protein cross-linking reveal the molecular architecture of these proteins in C* spliceosomes, providing mechanistic and structural insights into how they influence 3'ss usage. They further elucidate the path of the 3′ region of the intron, allowing a structure-based model for how the C* spliceosome potentially scans for the proximal 3′ss. By combining biochemical and structural approaches with genome-wide functional analyses, our studies reveal widespread regulation of alternative 3′ss usage after step 1 of splicing and the likely mechanisms whereby C* proteins influence NAGNAG 3′ss choices