Публикации ИЦиГ СО РАН 2015 год (в журналах с высоким импакт-фактором)

Публикации ИЦиГ в журналах с высоким импакт-фактором в 2015 году

Статьи ИЦиГ 2015 г. импакт факор >5

 

1. Identification of Bacillus strains by MALDI TOF MS using geometric approach.

Starostin KV, Demidov EA, Bryanskaya AV, Efimov VM, Rozanov AS, Peltek SE. Sci Rep. 2015 Nov 23;5: 16989.

IF 5.57

2. Inhibiting WEE1 Selectively Kills Histone H3K36me3-Deficient Cancers by dNTP Starvation.

Pfister SX, Markkanen E, Jiang Y, Sarkar S, Woodcock M, Orlando G, Mavrommati  I, Pai CC, Zalmas LP, Drobnitzky N, Dianov GL, Verrill C, Macaulay VM, Ying S, La Thangue NB, D’Angiolella V, Ryan AJ, Humphrey TC.

Cancer Cell. 2015 Oct 20.

IF 23.52

3. Global diversity, population stratification, and selection of human copy-number variation.

Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe

BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, Abdullah MS, Bravi CM, Capelli C, Hervig T, Wee JT, Tyler-Smith C, van Driem G, Romero IG, Jha AR, Karachanak-Yankova S, Toncheva D, Comas D, Henn B, Kivisild T, Ruiz-Linares A, Sajantila A, Metspalu E, Parik J, Villems R, Starikovskaya EB, Ayodo G, Beall CM, Di Rienzo A, Hammer MF, Khusainova R, K husnutdinova E, Klitz W, Winkler C, Labuda D, Metspalu M, Tishkoff SA, Dryomov S, Sukernik R, Patterson N, Reich D, Eichler EE.

Science 2015 Sep 11;349(6253): aab3761.. Epub 2015 Aug 6.

IF 33.61

4. Melatonin attenuates impairments of structural hippocampal neuroplasticity in OXYS rats during active progression of Alzheimer’s disease-like pathology.

Stefanova NA, Maksimova KY, Kiseleva E, Rudnitskaya EA, Muraleva NA, Kolosova NG.

J Pineal Res. 2015 Sep;59(2):163-77.

IF 9.6

5. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M,

Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, Damgaard Pde B, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T Jr, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CP, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E.

Science. 2015 Aug 21; 349(6250).

IF 33,61

6. Conditional mutations in Drosophila melanogaster: On the occasion of the 150th anniversary of G. Mendel’s report in Brünn.

Chadov BF, Fedorova NB, Chadova EV

Mutat Res Rev Mutat Res. 2015 Jul-Sep; 765:40-55.

IF 6,2

7. Nonadditive Effects of Genes in Human Metabolomics.

Tsepilov YA, Shin SY, Soranzo N, Spector TD, Prehn C, Adamski J, Kastenmüller

G, Wang-Sattler R, Strauch K, Gieger C, Aulchenko YS, Ried JS

Genetics. 2015 Jul; 200(3):707-18.

IF 5.96

8. Risk neurogenes for long-term spaceflight: dopamine and serotonin brain system.

Popova NK, Kulikov AV, Kondaurova EM, Tsybko AS, Kulikova EA, Krasnov IB, Shenkman BS, Bazhenova EY, Sinyakova NA, Naumenko VS.

Mol Neurobiol. 2015 Jun;51(3): 1443-51.

IF  5.14

9. Convergent evolution of ribonuclease h in LTR retrotransposons and retroviruses.

Ustyantsev K, Novikova O, Blinov A, Smyshlyaev G.

Mol Biol Evol. 2015 May;32(5):1197-207

IF  9,1

10. Disruption of Transcriptional Coactivator Sub1 Leads to Genome-Wide

Re-distribution of Clustered Mutations Induced by APOBEC in Active Yeast Genes.

Lada AG, Kliver SF, Dhar A, Polev DE, Masharsky AE, Rogozin IB, Pavlov YI.

PLoS Genet. 2015 May 5;11(5):

IF  7,53

11. Consortium. Inflammatory bowel disease associates with proinflammatory potential of the immunoglobulin G glycome.

Trbojević Akmačić I, Ventham NT, Theodoratou E, Vučković F, Kennedy NA,

Krištić J, Nimmo ER, Kalla R, Drummond H, Štambuk J, Dunlop MG, Novokmet M, Aulchenko Y, Gornik O, Campbell H, Pučić Baković M, Satsangi J, Lauc G; IBD-BIOM Inflamm Bowel Dis. 2015 Jun;21(6):1237-47.

IF  6.21

12. Amyloid accumulation is a late event in sporadic Alzheimer’s disease-like

pathology in nontransgenic rats.

Stefanova NA, Muraleva NA, Korbolina EE, Kiseleva E, Maksimova KY, Kolosova NG.

Oncotarget. 2015 Jan 30;6(3):1396-413.

IF  6.38

13. Cells deficient in base-excision repair reveal cancer hallmarks originating from adjustments to genetic instability.

Markkanen E, Fischer R, Ledentcova M, Kessler BM, Dianov GL. Nucleic Acids Res. 2015 Apr 20;43(7):3667-79.

IF  9,11

14. Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach.

Battulin N, Fishman VS, Mazur AM, Pomaznoy M, Khabarova AA, Afonnikov DA, Prokhortchouk EB, Serov OL.

Genome Biol. 2015 Apr 14;16:77.

IF  10.81

15. The genetic legacy of the expansion of Turkic-speaking nomads across Eurasia.

Yunusbayev B, Metspalu M, Metspalu E, Valeev A, Litvinov S, Valiev R, Akhmetova V, Balanovska E, Balanovsky O, Turdikulova S, Dalimova D, Nymadawa P, Bahmanimehr A, Sahakyan H, Tambets K, Fedorova S, Barashkov N, Khidiyatova I, Mihailov E, Khusainova R, Damba L, Derenko M, Malyarchuk B, Osipova L, Voevoda M, Yepiskoposyan L, Kivisild T, Khusnutdinova E, Villems R. PLoS Genet. 2015 Apr 21;11(4):

IF  7.53

16. A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S,

Ilumäe AM, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G, DeGiorgio M, Loogväli EL, Eichstaedt C, Eelmets M, Chaubey G, Tambets K, Litvinov S, Mormina M, Xue Y, Ayub Q, Zoraqi G, Korneliussen TS, Akhatova F, Lachance J, Tishkoff S, Momynaliev K, Ricaut FX, Kusuma P, Razafindrazaka H, Pierron D, Cox MP, Sultana GN, Willerslev R, Muller C, Westaway M, Lambert D, Skaro V, Kovačevic L, Turdikulova S, Dalimova D, Khusainova R, Trofimova N, Akhmetova V, Khidiyatova I, Lichman DV, Isakova J, Pocheshkhova E, Sabitov Z, Barashkov NA, Nymadawa P, Mihailov E, Seng JW, Evseeva I, Migliano AB, Abdullah S, Andriadze G, Primorac D, Atramentova L, Utevska O, Yepiskoposyan L, Marjanovic D, Kushniarevich A, Behar DM, Gilissen C, Vissers L, Veltman JA, Balanovska E, Derenko M, Malyarchuk B, Metspalu A, Fedorova S, Eriksson A, Manica A, Mendez FL, Karafet TM, Veeramah KR, Bradman N, Hammer MF,

Osipova LP, Balanovsky O, Khusnutdinova EK, Johnsen K, Remm M, Thomas MG, Tyler-Smith C, Underhill PA, Willerslev E, Nielsen R, Metspalu M, Villems R, Kivisild T. Genome Res. 2015 Apr;25(4):459-66.

IF  14.63

17. HMG-coenzyme A reductase inhibition, type 2 diabetes, and bodyweight: evidence from genetic analysis and randomised trials.

Swerdlow DI, Preiss D, Kuchenbaecker KB, Holmes MV, Engmann JE, Shah T, Sofat R, Stender S, Johnson PC, Scott RA, Leusink M, Verweij N, Sharp SJ, Guo Y, Giambartolomei C, Chung C, Peasey A, Amuzu A, Li K, Palmen J, Howard P, Cooper JA, Drenos F, Li YR, Lowe G, Gallacher J, Stewart MC, Tzoulaki I, Buxbaum SG, van der A DL, Forouhi NG, Onland-Moret NC, van der Schouw YT, Schnabel RB, HubacekJA, Kubinova R, Baceviciene M, Tamosiunas A, Pajak A, Topor-Madry R, Stepaniak U, Malyutina S, Baldassarre D, Sennblad B, Tremoli E, de Faire U, Veglia F, Ford I, Jukema JW, Westendorp RG, de Borst GJ, de Jong PA, Algra A, Spiering W, Maitland-van der Zee AH, Klungel OH, de Boer A, Doevendans PA, Eaton CB, Robinson JG, Duggan D; DIAGRAM Consortium; MAGIC Consortium; InterAct Consortium, Kjekshus J, Downs JR, Gotto AM, Keech AC, Marchioli R, Tognoni G, Sever PS, Poulter NR, Waters DD, Pedersen TR, Amarenco P, Nakamura H, McMurray JJ, Lewsey JD, Chasman DI, Ridker PM, Maggioni AP, Tavazzi L, Ray KK, Seshasai SR, Manson JE, Price JF, Whincup PH, Morris RW, Lawlor DA, Smith GD, Ben-Shlomo Y, Schreiner PJ, Fornage M, Siscovick DS, Cushman M, Kumari M, Wareham NJ, Verschuren WM, Redline S, Patel SR, Whittaker JC, Hamsten A, Delaney JA, Dale C, Gaunt TR, Wong A, Kuh D, Hardy R, Kathiresan S, Castillo BA, van der Harst P, Brunner EJ, Tybjaerg-Hansen A, Marmot MG, Krauss RM, Tsai M, Coresh J, Hoogeveen RC, Psaty BM, Lange LA, Hakonarson H, Dudbridge F, Humphries SE, Talmud PJ, Kivimäki M, Timpson NJ, Langenberg C, Asselbergs FW, Voevoda M, Bobak M, Pikhart H, Wilson JG, Reiner AP, Keating BJ, Hingorani AD, Sattar N.  Lancet. 2015 Jan 24;385(9965):351-61

IF  45.22

18. No DNA damage response and negligible genome-wide transcriptional changes in human embryonic stem cells exposed to terahertz radiation.

Bogomazova AN, Vassina EM, Goryachkovskaya TN, Popik VM, Sokolov AS, Kolchanov NA, Lagarkova MA, Kiselev SL, Peltek SE. Sci Rep. 2015 Jan 13;5:7749.

IF  5.58

19. FRIZZY PANICLE drives supernumerary spikelets in bread wheat.

Dobrovolskaya O, Pont C, Sibout R, Martinek P, Badaeva E, Murat F, Chosson A,

Watanabe N, Prat E, Gautier N, Gautier V, Poncet C, Orlov YL, Krasnikov AA,

Bergès H, Salina E, Laikova L, Salse J. Plant Physiol. 2015 Jan;167(1):189-99

IF  6,84

Январь — март 2015 года (Jan — Mar 2015)

Последние публикации ИЦиГ СО РАН

1.     Shishkina, Galina T.; Bulygina, Veta V.; Dygalo, Nikolay N.
Behavioral effects of glucocorticoids during the first exposures to the forced swim stress
PSYCHOPHARMACOLOGY Volume: 232   Issue: 5   Pages: 851-860   Published: MAR 2015
 
2.     Swerdlow, Daniel I.; Preiss, David; Kuchenbaecker, Karoline B.; et al.
HMG-coenzyme A reductase inhibition, type 2 diabetes, and bodyweight: evidence from genetic analysis and randomised trials
LANCET  Volume: 385   Issue: 9965   Pages: 351-361   Published: JAN 24 2015
 
3.     Bogomazova AN, Vassina EM, Goryachkovskaya TN, Popik VM, Sokolov AS, Kolchanov NA, Lagarkova MA, Kiselev SL, Peltek SE.
No DNA damage response and negligible genome-wide transcriptional changes in human embryonic stem cells exposed to terahertz radiation
SCIENTIFIC REPORTS  Volume: 5     Article Number: 7749   Published: JAN 13 2015
 
4.    Dobrovolskaya O, Pont C, Sibout R, Martinek P, Badaeva E, Murat F, Chosson A, Watanabe N, Prat E, Gautier N, Gautier V, Poncet C, Orlov YL, Krasnikov AA, Bergès H, Salina E, Laikova L, Salse J.
FRIZZY PANICLE Drives Supernumerary Spikelets in Bread Wheat
PLANT PHYSIOLOGY Volume: 167   Issue: 1   Pages: 189-199   Published: JAN 2015 

Март — июнь 2015 года (Mar — Jun 2015)

Последние публикации ИЦиГ СО РАН

1.  Beneficial effects of melatonin in a rat model of sporadic Alzheimer’s disease.

Rudnitskaya EA1, Maksimova KY, Muraleva NA, Logvinov SV, Yanshole LV, Kolosova NG, Stefanova NA.

Author information: Institute of Cytology and Genetics, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.

Biogerontology. 2015 Jun;16(3):303-16. doi: 10.1007/s10522-014-9547-7. Epub 2014 Dec 17.

Abstract

Melatonin synthesis is disordered in patients with Alzheimer’s disease (AD). To determine the role of melatonin in the pathogenesis of AD, suitable animal models are needed. The OXYS rats are an experimental model of accelerated senescence that has also been proposed as a spontaneous rat model of AD-like pathology. In the present study, we demonstrate that disturbances in melatonin secretion occur in OXYS rats at 4 months of age. These disturbances occur simultaneously with manifestation of behavioral abnormalities against the background of neurodegeneration and alterations in hormonal status but before the signs of amyloid-β accumulation. We examined whether oral administration of melatonin could normalize the melatonin secretion and have beneficial effects on OXYS rats before progression to AD-like pathology. The results showed that melatonin treatment restored melatonin secretion in the pineal gland of OXYS rats as well as the serum levels of growth hormone and IGF-1, the level of BDNF in the hippocampus and the healthy state of hippocampal neurons. Additionally, melatonin treatment of OXYS rats prevented an increase in anxiety and the decline of locomotor activity, of exploratory activity, and of reference memory. Thus, melatonin may be involved in AD progression, whereas oral administration of melatonin could be a prophylactic strategy to prevent or slow down the progression of some features of AD pathology.

2.  The influence of social environment in early life on the behavior, stress response, and reproductive system of adult male Norway rats selected for different attitudes to humans.

Gulevich RG, Shikhevich SG, Konoshenko MY, Kozhemyakina RV, Herbeck YE, Prasolova LA, Oskina IN, Plyusnina IZ.

Physiol Behav. 2015 May 15;144:116-23. doi: 10.1016/j.physbeh.2015.03.018. Epub 2015 Mar 14.

Abstract

The influence of social disturbance in early life on behavior, response of blood corticosterone level to restraint stress, and endocrine and morphometric indices of the testes was studied in 2-month Norway rat males from three populations: not selected for behavior (unselected), selected for against aggression to humans (tame), and selected for increased aggression to humans (aggressive). The experimental social disturbance included early weaning, daily replacement of cagemates from days 19 to 25, and subsequent housing in twos till the age of 2months. The social disturbance increased the latent period of aggressive behavior in the social interaction test in unselected males and reduced relative testis weights in comparison to the corresponding control groups. In addition, experimental unselected rats had smaller diameters of seminiferous tubules and lower blood testosterone levels. In the experimental group, tame rats had lower basal corticosterone levels, and aggressive animals had lower hormone levels after restraint stress in comparison to the control. The results suggest that the selection in two directions for attitude to humans modifies the response of male rats to social disturbance in early life. In this regard, the selected rat populations may be viewed as a model for investigation of (1) neuroendocrinal mechanisms responsible for the manifestation of aggression and (2) interaction of the hypothalamic-pituitary-adrenal and hypothalamic-pituitary-gonadal systems in stress.

3.  MtDNA Haplogroup A10 Lineages in Bronze Age Samples Suggest That Ancient Autochthonous Human Groups Contributed to the Specificity of the Indigenous West Siberian Population.

Pilipenko AS1, Trapezov RO2, Zhuravlev AA2, Molodin VI3, Romaschenko AG4.

PLoS One. 2015 May 7;10(5):e0127182. doi: 10.1371/journal.pone.0127182. eCollection 2015. 

Abstract

BACKGROUND:

The craniometric specificity of the indigenous West Siberian human populations cannot be completely explained by the genetic interactions of the western and eastern Eurasian groups recorded in the archaeology of the area from the beginning of the 2nd millennium BC. Anthropologists have proposed another probable explanation: contribution to the genetic structure of West Siberian indigenous populations by ancient human groups, which separated from western and eastern Eurasian populations before the final formation of their phenotypic and genetic features and evolved independently in the region over a long period of time. This hypothesis remains untested. From the genetic point of view, it could be confirmed by the presence in the gene pool of indigenous populations of autochthonous components that evolved in the region over long time periods. The detection of such components, particularly in the mtDNA gene pool, is crucial for further clarification of early regional genetic history.

RESULTS AND CONCLUSION:

We present the results of analysis of mtDNA samples (n = 10) belonging to the A10 haplogroup, from Bronze Age populations of West Siberian forest-steppe (V-I millennium BC), that were identified in a screening study of a large diachronic sample (n = 96). A10 lineages, which are very rare in modern Eurasian populations, were found in all the Bronze Age groups under study. Data on the A10 lineages’ phylogeny and phylogeography in ancient West Siberian and modern Eurasian populations suggest that A10 haplogroup underwent a long-term evolution in West Siberia or arose there autochthonously; thus, the presence of A10 lineages indicates the possible contribution of early autochthonous human groups to the genetic specificity of modern populations, in addition to contributions of later interactions of western and eastern Eurasian populations.

4.   A genome wide association study links glutamate receptor pathway to sporadic creutzfeldt-jakob disease risk.[САЮ1] 

Sanchez-Juan P, Bishop MT, Kovacs GG, Calero M, Aulchenko YS, Ladogana A, Boyd A, Lewis V, Ponto C, Calero O, Poleggi A, Carracedo Á, van der Lee SJ, Ströbel T, Rivadeneira F, Hofman A, Haïk S, Combarros O, Berciano J, Uitterlinden AG, Collins SJ, Budka H, Brandel JP, Laplanche JL, Pocchiari M, Zerr I, Knight RS, Will RG, van Duijn CM.

PLoS One. 2015 Apr 28;10(4):e0123654. doi: 10.1371/journal.pone.0123654. eCollection 2014.

Abstract

We performed a genome-wide association (GWA) study in 434 sporadic Creutzfeldt-Jakob disease (sCJD) patients and 1939 controls from the United Kingdom, Germany and The Netherlands. The findings were replicated in an independent sample of 1109 sCJD and 2264 controls provided by a multinational consortium. From the initial GWA analysis we selected 23 SNPs for further genotyping in 1109 sCJD cases from seven different countries. Five SNPs were significantly associated with sCJD after correction for multiple testing. Subsequently these five SNPs were genotyped in 2264 controls. The pooled analysis, including 1543 sCJD cases and 4203 controls, yielded two genome wide significant results: rs6107516 (p-value=7.62×10-9) a variant tagging the prion protein gene (PRNP); and rs6951643 (p-value=1.66×10-8) tagging the Glutamate Receptor Metabotropic 8 gene (GRM8). Next we analysed the data stratifying by country of origin combining samples from the pooled analysis with genotypes from the 1000 Genomes Project and imputed genotypes from the Rotterdam Study (Total n=12967). The meta-analysis of the results showed that rs6107516 (p-value=3.00×10-8) and rs6951643 (p-value=3.91×10-5) remained as the two most significantly associated SNPs. Rs6951643 is located in an intronic region of GRM8, a gene that was additionally tagged by a cluster of 12 SNPs within our top100 ranked results. GRM8 encodes for mGluR8, a protein which belongs to the metabotropic glutamate receptor family, recently shown to be involved in the transduction of cellular signals triggered by the prion protein. Pathway enrichment analyses performed with both Ingenuity Pathway Analysis and ALIGATOR postulates glutamate receptor signalling as one of the main pathways associated with sCJD. In summary, we have detected GRM8 as a novel, non-PRNP, genome-wide significant marker associated with heightened disease risk, providing additional evidence supporting a role of glutamate receptors in sCJD pathogenesis.

5.  Cells deficient in base-excision repair reveal cancer hallmarks originating from adjustments to genetic instability[САЮ2] .

Markkanen E, Fischer R, Ledentcova M, Kessler BM, Dianov GL.

Nucleic Acids Res. 2015 Apr 20;43(7):3667-79. doi: 10.1093/nar/gkv222. Epub 2015 Mar 23.

Abstract

Genetic instability, provoked by exogenous mutagens, is well linked to initiation of cancer. However, even in unstressed cells, DNA undergoes a plethora of spontaneous alterations provoked by its inherent chemical instability and the intracellular milieu. Base excision repair (BER) is the major cellular pathway responsible for repair of these lesions, and as deficiency in BER activity results in DNA damage it has been proposed that it may trigger the development of sporadic cancers. Nevertheless, experimental evidence for this model remains inconsistent and elusive. Here, we performed a proteomic analysis of BER deficient human cells using stable isotope labelling with amino acids in cell culture (SILAC), and demonstrate that BER deficiency, which induces genetic instability, results in dramatic changes in gene expression, resembling changes found in many cancers. We observed profound alterations in tissue homeostasis, serine biosynthesis, and one-carbon- and amino acid metabolism, all of which have been identified as cancer cell ‘hallmarks’. For the first time, this study describes gene expression changes characteristic for cells deficient in repair of endogenous DNA lesions by BER. These expression changes resemble those observed in cancer cells, suggesting that genetically unstable BER deficient cells may be a source of pre-cancerous cells.

6.  Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach.

Battulin N, Fishman VS, Mazur AM, Pomaznoy M, Khabarova AA, Afonnikov DA, Prokhortchouk EB, Serov OL.

Genome Biol. 2015 Apr 14;16(1):77. doi: 10.1186/s13059-015-0642-0.

Abstract

BACKGROUND:

The three-dimensional organization of the genome is tightly connected to its biological function. The Hi-C approach was recently introduced as a method that can be used to identify higher-order chromatin interactions genome-wide. The aim of this study was to determine genome-wide chromatin interaction frequencies using the Hi-C approach in mouse sperm cells and embryonic fibroblasts.

RESULTS:

The obtained data demonstrate that the three-dimensional genome organizations of sperm and fibroblast cells show a high degree of similarity both with each other and with the previously described mouse embryonic stem cells. Both A- and B-compartments and topologically associated domains are present in spermatozoa and fibroblasts. Nevertheless, sperm cells and fibroblasts exhibit statistically significant differences between each other in the contact probabilities of defined loci. Tight packaging of the sperm genome results in an enrichment of long-range contacts compared with the fibroblasts. However, only 30% of the differences in the number of contacts are based on differences in the densities of their genome packages; the main source of the differences is the gain or loss of contacts that are specific for defined genome regions. We find that the dependence of the contact probability on genomic distance for sperm is close to the dependence predicted for the fractal globular folding of chromatin.

CONCLUSIONS:

Overall, we can conclude that the three-dimensional structure of the genome is passed through generations without being dramatically changed in sperm cells.

7.     The genetic legacy of the expansion of Turkic-speaking nomads across Eurasia.

Yunusbayev B, Metspalu M, Metspalu E, Valeev A, Litvinov S, Valiev R, Akhmetova V, Balanovska E, Balanovsky O, Turdikulova S, Dalimova D8, Nymadawa P9, Bahmanimehr A10, Sahakyan H11, Tambets K, Fedorova S, Barashkov N, Khidiyatova I, Mihailov E, Khusainova R, Damba L, Derenko M, Malyarchuk B, Osipova L, Voevoda M, Yepiskoposyan L, Kivisild T, Khusnutdinova E, Villems R.

PLoS Genet. 2015 Apr 21;11(4):e1005068. doi: 10.1371/journal.pgen.1005068. eCollection 2015.

Abstract

The Turkic peoples represent a diverse collection of ethnic groups defined by the Turkic languages. These groups have dispersed across a vast area, including Siberia, Northwest China, Central Asia, East Europe, the Caucasus, Anatolia, the Middle East, and Afghanistan. The origin and early dispersal history of the Turkic peoples is disputed, with candidates for their ancient homeland ranging from the Transcaspian steppe to Manchuria in Northeast Asia. Previous genetic studies have not identified a clear-cut unifying genetic signal for the Turkic peoples, which lends support for language replacement rather than demic diffusion as the model for the Turkic language’s expansion. We addressed the genetic origin of 373 individuals from 22 Turkic-speaking populations, representing their current geographic range, by analyzing genome-wide high-density genotype data. In agreement with the elite dominance model of language expansion most of the Turkic peoples studied genetically resemble their geographic neighbors. However, western Turkic peoples sampled across West Eurasia shared an excess of long chromosomal tracts that are identical by descent (IBD) with populations from present-day South Siberia and Mongolia (SSM), an area where historians center a series of early Turkic and non-Turkic steppe polities. While SSM matching IBD tracts (> 1cM) are also observed in non-Turkic populations, Turkic peoples demonstrate a higher percentage of such tracts (p-values ≤ 0.01) compared to their non-Turkic neighbors. Finally, we used the ALDER method and inferred admixture dates (~9th-17th centuries) that overlap with the Turkic migrations of the 5th-16th centuries. Thus, our results indicate historical admixture among Turkic peoples, and the recent shared ancestry with modern populations in SSM supports one of the hypothesized homelands for their nomadic Turkic and related Mongolic ancestors.

8. A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

Karmin , Saag , Vicente , Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G, DeGiorgio M, Loogväli EL, Eichstaedt C, Eelmets M, Chaubey G, Tambets K, Litvinov S, Mormina M, Xue Y, Ayub Q, Zoraqi G, Korneliussen TS, Akhatova F, Lachance J, Tishkoff S, Momynaliev K, Ricaut FX, Kusuma P, Razafindrazaka H, Pierron D, Cox MP, Sultana GN, Willerslev R, Muller C, Westaway M, Lambert D, Skaro V, Kovačevic L, Turdikulova S, Dalimova D, Khusainova R, Trofimova N, Akhmetova V, Khidiyatova I, Lichman DV, Isakova J, Pocheshkhova E, Sabitov Z, Barashkov NA, Nymadawa P, Mihailov E, Seng JW, Evseeva I, Migliano AB, Abdullah S, Andriadze G, Primorac D, Atramentova L, Utevska O, Yepiskoposyan L, Marjanovic D, Kushniarevich A, Behar DM, Gilissen C, Vissers L, Veltman JA, Balanovska E, Derenko M, Malyarchuk B, Metspalu A, Fedorova S, Eriksson A, Manica A, Mendez FL, Karafet TM, Veeramah KR, Bradman N, Hammer MF, Osipova LP, Balanovsky O, Khusnutdinova EK, Johnsen K, Remm M, Thomas MG, Tyler-Smith C, Underhill PA, Willerslev E, Nielsen R, Metspalu M, Villems R, Kivisild T.

Genome Res. 2015 Apr;25(4):459-66. doi: 10.1101/gr.186684.114. Epub 2015 Mar 13.

Abstract

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.