last update: April 2012

With experimental high-throughput cDNA library screening and biocomputational methods we identify and characterize novel npcRNAs from diverse model organisms. In contrast to mRNAs, which are templates for translating proteins, npcRNAs exhibit various functions in different compartments and developmental stages of the cell. Small nucleolar RNAs (snoRNAs), one of the largest classes of npcRNAs, guide post-transcriptional modifications of other RNAs that are crucial for appropriate RNA folding as well as for RNA-RNA and RNA-protein interactions. Detailed comparisons of paralog snoRNAs revealed, in addition to trans-duplication, a novel, cis-duplication distribution strategy with insertions near to the original loci. Some snoRNAs coevolved with their modification target sites, demonstrating the close interaction of complementary regions. Some target sites modified by snoRNAs are changed, added or lost, documenting a high degree of evolutionary plasticity of npcRNAs. The evolutionary history of npcRNAs in mammalian species is one of our main subjects to explore the world of RNomics.

Reconstruction of the placental mammalian (eutherian) evolutionary tree has undergone diverse revisions and numerous aspects remain hotly debated. Initial hierarchical divisions based on morphology contained many misgroupings due to features that evolved independently by similar selection processes. Molecular analyses corrected many of these misgroupings and the superordinal hierarchy of placental mammals was recently assembled into four clades. However, long or rapid evolutionary periods as well as directional mutation pressure can produce molecular homoplasies, similar characteristics lacking common ancestors.
Retroposed elements, by contrast, integrate randomly into genomes with negligible probabilities of the same element integrating independently into orthologous positions in different species. Thus, presence/absence analyses of these elements are a superior strategy for molecular systematics.

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Selected References:

2012
52.	Suh A, Kriegs JO, Donnellan S, Brosius J, Schmitz J. A universal method for the study of CR1 retroposons in non-model bird genomes Mol Biol Evol, in press
51.	Schmitz J Review: SINEs as driving forces in genome evolution Genome Dynamics, in press
50.	Matzke A, Churakov G, Berkes P, Arms E, Kelsey D, Brosius J, Kriegs JO, Schmitz J Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era Mol Biol Evol, in press
49.	Erpenbeck D, Schmitz J, Churakov G, Huchon D, Wöhrheide G, Degnan BM First evidence of miniature transposable elements in Porifera Hydrobiology 687:43-47
2011
48.	Schmitz J, Brosius J Review: Exonization of transposed elements: A challenge and opportunity for evolution Biochimie 93:1928-1934 (pdf)
47.	Suh A, Paus M, Kiefmann M, Churakov G, Franke FA, Brosius J, Kriegs JO, Schmitz J Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds Nat Commun 2:443 (pdf)
46.	Suh A, Kriegs JO, Brosius J, Schmitz J Retroposon insertions and the chronology of avian sex chromosome evolution Mol Biol Evol, 28:2993-2997 (pdf)
2010
45.	Churakov G, Grundmann N, Kuritzin A, Brosius J, Makałowski W , Schmitz J Software: A novel web-based TinT application and the chronology of the primate Alu retroposon activity BMC Evol Biol, 10:376 (pdf)
44.	Kriegs JO, Zemann A, Churakov G, Matzke A, Ohme M, Zischler H, Brosius J, Kryger U, Schmitz J Retroposon insertions provide insights into deep lagomorph evolution Mol Biol Evol, 27:2678-2681 (pdf)
43.	Nilsson M, Churakov G, Sommer M, Ngoc Van T, Zemann A, Brosius J, Schmitz J Tracking marsupial evolution using archaic genomic retroposon insertions PLoS Biol 8:e1000436 (pdf)
42.	Churakov G, Sadasivuni M, Rosenbool K, Huchon D, Brosius J, Schmitz J Rodent Evolution: Back to the Root Mol Biol Evol 27:1315-1326 (pdf)
2009
41.	Churakov G, Kriegs JO, Baertsch R, Zemann A, Brosius J, Schmitz J Mosaic retroposon insertion patterns in placental mammals Genome Res 19:868-875 (pdf)
2008
40.	Moeller-Krull M, Zemann A, Roos C, Brosius J, Schmitz J Beyond DNA: RNA-editing and steps toward Alu-exonization in primates J Mol Biol 382:601-609 (pdf)
39.	Warren WC, Hillier LW, Graves JAM, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang S-P, Heager A, Clarke D, Miethke P, Waters P, Veyrunes F, Fulton L, Graves T, Puente X, Lopez-Otin C, Ordonez GR, Eichler EE,  Deakin JE, Thompson K, Kirby P, Papenfuss AT, Wakefield M, Olender T, Lancet D, Huttley GA, Smit AFA, Renfree M, Temple-Smith P, Batzer MA, Jerilyn A, Walker JA, Konkel MK, Harris RS, Taylor J, Whittington CM, Gemmell N, Buschiazzo E, Jentzsch IV, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison E, Sachidanandam R, Smith C, Stark A, Hannon G, Rens W, Ferguson-Smith M, Lefevre C, Sharp J, Nicholas KR, Ray D, Kube M, Reinhardt R, Pringle TH, Flicek P, Washington University Genome Sequencing Center, Mardis ER, Wilson RK Genome analysis of the platypus reveals unique signatures of evolution Nature 453:175-184 (pdf)
38.	Schmitz J, Zemann A, Churakov G, Kuhl H, Grützner F, Reinhardt R, Brosius J Retroposed SNOfall – A mammalian-wide comparison of platypus snoRNAs Genome Res 18:1005-1010 (pdf)
37.	Qiu H, Taudien S, Herlyn H, Schmitz J, Zhou Y, Chen G, Roberto R, Rocchi M, Platzer M, Wojnowski L CYP3 phylogenomics: Evidence for positive selection of CYP3A4 and CYP3A7 Pharmacogenetics and Genomics 18:53-66 (pdf)
2007
36.	Kriegs JO, Matzke A, Churakov G, Kuritzin A, Mayr G, Brosius J, Schmitz J Waves of genomic hitchhikers characterize the evolution of gamebirds (Aves: Galliformes) BMC Evol Biol 7:190 (pdf)
35.	Möller-Krull M, Delsuc F, Churakov G, Marker C, Superina M, Brosius J, Douzery EJP, Schmitz J Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters and sloths) Mol Biol Evol 24:2573-2582 (pdf)
34.	Chen X, Collins L, Rozhdestvensky TS, Schmitz J, Penny D Combined experimental and computional approach to identify non-protein-coding RNAs in the deep branching eukaryote Giardia intestinalis Nucleic Acids Res 35:4619-4628 (pdf)
33.	Krull M, Petrusma M, Makalowski W, Brosius J, Schmitz J Functional persistence of exonized Mammalian-wide Interspersed Repeat elements (MIRs) Genome Res 17:1139-1145 (pdf)
32.	Huchon D, Chevret P, Jordan U, Kilpatrick CW, Ranwez V, Jenkins PD, Brosius J, Schmitz J Multiple molecular evidence for a living mammalian fossil Proc Natl Acad Sci USA 104:7495-7499 (pdf)
31.	Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J Evolutionary history of 7SL RNA-derived SINEs in Supraprimates - Glires and Euarchonta Phylogeny - Trends Genet 23:158-161 (pdf)
2006
30.	Farwick A, Jordan U, Fuellen G, Huchon D,  Catzeflis F, Brosius J, Schmitz J Automated scanning for phylogenetically informative transposed elements in rodents Sys Biol 55:936-948 (pdf)
29.	Kuryshev VY, Vorobyov E, Zink D, Schmitz J, Rozhdestvensky TS, Münstermann E, Ernst U, Wellenreuther R, Moosmayer P, Bechtel S, Schupp I, Hort J, Korn B, Poustka A, Wiemann S An anthropoid-specific segmental duplication on human chromosome 1q22: Structure and evolution of the affected genes Genomics 88:143-151 (pdf)
28.	Zemann A, op de Bekke A, Kiefmann M, Brosius J, Schmitz J  Evolution of small nucleolar RNAs in nematodes Nucleic Acids Res 34:2676-2685 (pdf, supplemental data)
27.	Kriegs JO, Churakov G, Kiefmann M, Jordan U,  Brosius J, Schmitz J  Retropsosed elements as archives for the evolutionary history of placental  mammals PLoS Biol 4:e91 (pdf, supplemental data)
2005
26.	Schmitz J, Piskurek O, Zischler H    40 Million years of independent evolution: a mitochondrial gene and its  corresponding nuclear pseudogene in primates J Mol Evol 61:1-11 (pdf, supplemental data)
25.	Krull M, Brosius J, Schmitz J     Alu-SINE exonization: en route to protein-coding function Mol Biol Evol 22:1702-1711 (pdf, supplemental data)
24.	Churakov G, Smit A, Brosius J, Schmitz J A novel abundant family of transposable elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus). Mol Biol Evol 22:886-893 (pdf, supplemental data)
23.	Ludwig A, Rozhdestvensky TS, Kuryshev V,  Schmitz J, Brosius J An unusual primate locus that attracted two independent Alu insertions and facilitates their transcription. J Mol Biol 350:200-214 (pdf)
22.	Kriegs JO, Schmitz J, Makalowski W, Brosius J Does the AD7c-NTP locus encode a protein? BBA 1727:1-4 (pdf)
21.	Schmitz J, Roos C, Zischler H Primate phylogeny: Molecular evidence from retroposons Cyt Genome Res 108:26-37 (pdf)
2004
20.	Schmitz J, Churakov G, Zischler H, Brosius J A novel class of tailless retropseudogenes in mammalian genomes. Genome Res 14:1911-1015 (pdf, supplemental data)
19.	Singer SS, Maennel, DN, Hehlgans T, Brosius J, Schmitz J From “junk“ to Gene: Curriculum vitae of a primate receptor isoform gene J Mol Biol 341:883-886 (pdf)
18.	Roos C, Schmitz J, Zischler H Primate jumping genes elucidate strepsirrhine phylogeny Proc Natl Acad Sci USA 101:10650-10654 (pdf)
17.	Schmitz J, Zischler H Molecular cladistic markers and the infraordinal phylogenetic relationships of primates. In: Anthropoid Origins: New Visions, Kay, RF, Ross, C (eds), Kluwer Academic Press, NY (information)
2003
16.	Schmitz J, Zischler H Analysis of retrotransposons in dermopterans uncover a new family of tRNA-derived SINEs and support a monopyletic origin of the order primates Mol Phyl Evol 28:341-349 (pdf)
15.	Singer SS, Schmitz J, Schwiegk C, Zischler H Molecular cladistic markers in New World monkey phylogeny (Platyrrhini, Primates) Mol Phyl Evol 26:490-501 (pdf)
14.	Herlyn H, Piskurek O, Schmitz J, Ehlers U, Zischler H The syndermatan phylogeny and the evolution of acanthocephalan endoparasitism as inferred from 18S rDNA sequences Mol Phyl Evol 26:155-164 (pdf)
2002
13.	Albert S, Schmitz J Characterization of the major royal jelly family like DNA sequences in Apis dorsata J Apic Res 41:75-82 (pdf)
12.	Schmitz J, Ohme M, Suryobroto B, Zischler H The colugo (Cynocephalus variegatus, Dermoptera): The Primates‘ gliding sister? Mol Biol Evol 19:2308-2312 (pdf)
11.	Schmitz J, Ohme M, Zischler H The complete mitochondrial sequence of Tarsius bancanus: evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA Mol Biol Evol 19:544-553 (pdf)
2001
10.	Schmitz J, Ohme M, Zischler H SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates Genetics 157:777-784 (pdf)
2000
9.	Schmitz J, Ohme M, Zischler H The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of Scandentia to other eutherian orders Mol Biol Evol 17, 1334-1343 (pdf)
8.	Schmitz J, Moritz RFA Molecular evolution in social wasps. In: Hymenoptera: Evolution, biodiversity and biological control Austin AD, Dowton M (eds) pp 84-89, CSIRO Publishing, Collingwood (information)
7.	Weichhardt-Kulessa K, Börner T, Schmitz J, Müller-Doblies U, Müller-Doblies D Controversial taxonomy of Strumariinae (Amaryllidaceae) investigated by nuclear rDNA (IST) sequences Plant Syst Evol 223:1-13 (abstract)
1998
6.	Schmitz J, Moritz RFA Sociality and the rate of rDNA sequence evolution in wasps (Vespidae) and honeybees (Apis) J Mol Evol 47, 606-612 (pdf)
5.	Schmitz J, Moritz RFA Molecular phylogeny of Vespidae (Hymenoptera) and the evolution of sociality in wasps Mol Phyl Evol 9:183-191 (pdf)
1994
4.	Schmitz J, Moritz RFA Sequence analysis of the D1 and D2 regions of 28S rDNA in the hornet (Vespa crabro, Hymenoptera, Vespinae) Insect Mol Biol 3:273-277 (pdf)
1990
3.	Schmitz J Restriction enzyme analysis of mitochondrial DNA of wasps (Vespinae) Apidologie 21:335-336
2.	Schmitz J, Moritz RFA Mitochondrial DNA variation in social wasps (Hymenoptera, Vespidae) Experientia 46:1068-1072 (pdf)
1989
1.	Schmitz J Mitochondrial DNA in social wasps Apidologie 20:529-531

Additonal References:

Lewejohann L, Skryabin BV, Sachser N, Prehn C, Heiduschka P, Thanos S, Jordan U,  Dell'Omo G, Vyssotski AL, Pleskacheva MG, Lipp HP, Tiedge H, Brosius J, Prior H 2004
Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice
Behav Brain Res 154:273-289

Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A, Wagner EG 2003
RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria
Nucleic Acids Res 31:6435-43

Skryabin BV, Sukonina V, Jordan U, Lewejohann L, Sachser N, Muslimov I, Tiedge H, Brosius J 2003
Neuronal untranslated BC1 RNA: targeted gene elimination in mice
Mol Cell Biol 2003 23:6435-6441

Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P, Bachellerie JP, Brosius J, Huttenhofer A 2002
Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana
Curr Biol 12:2002-2013