Mammal Sites Research Articles

Updating the fauna and age of the Neogene-Quaternary large mammal sites of Greece

The Neogene-Quaternary continental deposits cover large areas of Greece and several fossil mammal sites have been discovered in the country. There are several collections of large fossil mammals for this time span, which provide important data for the fauna biochronology, correlations, palaeoecology and palaeogeography of the area. The last lists with the fauna, age and biochronology of the Greek large mammal localities were given in 2006 for the Neogene and in 2001 for the Quaternary. Extensive research over the last twenty years provided several new localities, and many data and information were published. Therefore, an updating of the lists was more than necessary, and the present article deals with it; it covers the time span untill June 2023. Lists include all faunal information as the systematic classification, chronology, biostratigraphic correlation of the faunas, and main bibliography. It is worth mentioning that some of the Greek localities are key-localities for the Eastern Mediterranean region, e.g., Pikermi, Axios Valley, Villafranchian collection. These faunas are important for the comparison and identification of new collections, correlations, palaeoecology, and palaeogeography of Neogene European mammals.

The Occurrence of Suids in the Post-Olduvai to Pre-Jaramillo Pleistocene of Europe and Implications for Late Villafranchian Biochronology and Faunal Dynamics

It has been proposed that suids were absent from Europe during the post-Olduvai to pre-Jaramillo Early Pleistocene (from less than 1.8 to more than 1.2 Ma) and that their “re-appearance” in the late Early Pleistocene would mark the end of the late Villafranchian and the beginning of the Epivillafranchian. Arguments enumerated in favor of this “suid gap” are the lack of suid remains from extensively sampled fossil localities of this age and the high reproductive potential (r-strategy) of suids, which would translate in a high commonness of their remains in the fossil record. However, here it shown that while suids’ reproductive potential is certainly exceptional within artiodactyls, there is no direct relationship between the reproductive strategy and preservation rate of a taxon in the fossil record. In Early Pleistocene localities of Europe and adjoining areas, where suids are present in a fossil assemblage, they are always rare. In terms of number of occurrences (frequency), suids range from being moderately common (~2.0–1.8 Ma) to moderately rare (~1.1–1.0 Ma). Suid material is also described herein from Peyrolles (Issoire, France; reference locality for MNQ 19), a site dated at 1.47 Ma, providing direct evidence for the presence of suids within the purported “suid gap”. The case of suids underlines an important source of caveat in inferring faunal dynamics of the late Early Pleistocene of western Europe—including the dispersal of hominins—i.e., the unequal geographical distribution of the paleontological sites of post-Olduvai to pre-Jaramillo age. Indeed, Peyrolles is the only large mammal site in western Europe located outside the Iberian and Italian Peninsulas reliably dated around 1.5 Ma. In the post-Olduvai to pre-Jaramillo period, there is a paucity of radiometric estimates (or they have too coarse a resolution) and of paleomagnetic excursions detectable in continental deposits. Basically, for this time span, there is a high dependence on biochronological correlations, although, at the same time, these correlations are less reliable—because these are based on a few sites not covering the entire spectrum of environments present in Europe and the sites are not independently dated with methods that outperform biochronology—than those for other periods.

Mitochondrial lipid dynamics regulated by MITOL-mediated ubiquitination.

Mitochondria-endoplasmic reticulum (ER) contact sites in mammals provide platforms for various reactions, such as calcium signaling, lipid metabolism, organelle dynamics and autophagy. To fulfill these tasks, a number of proteins assemble at the contact sites including MITOL/MARCHF5, a critical mitochondrial ubiquitin ligase. How MITOL regulates mitochondrial function from the contact site, however, has been largely unresolved. Recently, a new role for MITOL in the active transport of phosphatidic acid from the ER to mitochondria was reported. In this commentary, we briefly summarize our current understanding of mitochondria-ER contact sites and discuss the recently elucidated mechanism of MITOL fine-tuning phospholipid transfer activity through ubiquitination.

GR-m6A: Prediction of N6-methyladenosine sites in mammals with molecular graph and residual network

RNA N6-methyladenine (m6A), which is produced by the methylation of the N6 position of eukaryotic adenine, is a relatively common post-transcriptional modification on the surface of the molecule, which frequently plays a crucial role in biological processes. Biological experimental methods to identify m6A have been studied and implemented in recent years, but they cannot be promoted widely due to drawbacks such as the time and cost of reagents and equipment. Therefore, researchers have proposed computational strategies for identifying m6A sites, but these strategies do not account for the mechanism of methylation occurrence or the structure of RNA molecules. This study, therefore, proposed a novel deep learning model for predicting m6A sites, GR-m6A, which predicts m6A sites by extracting features from the physicochemical properties and spatial structure of molecules via residual networks. In GR-m6A, each RNA base string is represented by SMILES as two matrices comprising topology structural information and node attributes with molecular physicochemical characteristics. The feature encoding matrix was then obtained by fusing the topology matrix and the node matrix in accordance with the graphical convolutional network principle. Correspondingly, the more discriminative features were extracted from the encoding matrix using the residual neural network and predicted using a multilayer perceptron. As evident from the 5-fold cross-validation and independent validation, the GR-m6A model outperformed other existing methods. Thus, we hope that GR-m6A can aid researchers in predicting mammalian m6A loci. The source code and database are available at https://github.com/YingLiangjxau/GR-m6A.

O-166 Distinct molecular signatures of successful sperm in situ

Abstract Out of millions of ejaculated sperm, a few reach the fertilization site in mammals. Flagellar Ca2+ signaling nanodomains, organized by multi-subunit CatSper calcium channel complexes, are pivotal for sperm migration in the female tract, implicating CatSper-dependent mechanisms in sperm selection. Here using biochemical and pharmacological studies, we demonstrate that CatSper1 is an O-linked glycosylated protein, undergoing capacitation-induced processing dependent on Ca2+ and phosphorylation cascades. CatSper1 processing correlates with protein tyrosine phosphorylation (pY) development in sperm cells capacitated in vitro and in vivo. Using 3D in situ molecular imaging and ANN-based automatic detection of sperm distributed along the cleared female tract, we demonstrate that spermatozoa past the utero-tubal junction possess the intact CatSper1 signals. Together, we reveal that fertilizing mouse spermatozoa in situ are characterized by intact CatSper channel, lack of pY, and reacted acrosomes. These findings provide molecular insight into sperm selection for successful fertilization in the female reproductive tract.

Oldest evidence of abundant C 4 grasses and habitat heterogeneity in eastern Africa

The assembly of Africa's iconic C4 grassland ecosystems is central to evolutionary interpretations of many mammal lineages, including hominins. C4 grasses are thought to have become ecologically dominant in Africa only after 10 million years ago (Ma). However, paleobotanical records older than 10 Ma are sparse, limiting assessment of the timing and nature of C4 biomass expansion. This study uses a multiproxy design to document vegetation structure from nine Early Miocene mammal site complexes across eastern Africa. Results demonstrate that between ~21 and 16 Ma, C4 grasses were locally abundant, contributing to heterogeneous habitats ranging from forests to wooded grasslands. These data push back the oldest evidence of C4 grass-dominated habitats in Africa-and globally-by more than 10 million years, calling for revised paleoecological interpretations of mammalian evolution.

DL-m6A: Identification of N6-Methyladenosine Sites in Mammals Using Deep Learning Based on Different Encoding Schemes.

N6-methyladenosine (m6A) is a common post-transcriptional alteration that plays a critical function in a variety of biological processes. Although experimental approaches for identifying m6A sites have been developed and deployed, they are currently expensive for transcriptome-wide m6A identification. Some computational strategies for identifying m6A sites have been presented as an effective complement to the experimental procedure. However, their performance still requires improvement. In this study, we have proposed a novel tool called DL-m6A for the identification of m6A sites in mammals using deep learning based on different encoding schemes. The proposed tool uses three encoding schemes which give the required contextual feature representation to the input RNA sequence. Later these contextual feature vectors individually go through several neural network layers for shallow feature extraction after which they are concatenated to a single feature vector. The concatenated feature map is then used by several other layers to extract the deep features so that the insight features of the sequence can be used for the prediction of m6A sites. The proposed tool is firstly evaluated on the tissue-specific dataset and later on a full transcript dataset. To ensure the generalizability of the tool we assessed the proposed model by training it on a full transcript dataset and test on the tissue-specific dataset. The achieved results by the proposed model have outperformed the existing tools. The results demonstrate that the proposed tool can be of great use for the biology experts and therefore a freely accessible web-server is created which can be accessed at: http://nsclbio.jbnu.ac.kr/tools/DL-m6A/.

Alternative splicing modulation by G-quadruplexes

Alternative splicing is central to metazoan gene regulation, but the regulatory mechanisms are incompletely understood. Here, we show that G-quadruplex (G4) motifs are enriched ~3-fold near splice junctions. The importance of G4s in RNA is emphasised by a higher enrichment for the non-template strand. RNA-seq data from mouse and human neurons reveals an enrichment of G4s at exons that were skipped following depolarisation induced by potassium chloride. We validate the formation of stable RNA G4s for three candidate splice sites by circular dichroism spectroscopy, UV-melting and fluorescence measurements. Moreover, we find that sQTLs are enriched at G4s, and a minigene experiment provides further support for their role in promoting exon inclusion. Analysis of >1,800 high-throughput experiments reveals multiple RNA binding proteins associated with G4s. Finally, exploration of G4 motifs across eleven species shows strong enrichment at splice sites in mammals and birds, suggesting an evolutionary conserved splice regulatory mechanism.

My home is your home: Nest boxes for birds and mammals provide habitats for diverse insect communities

Abstract Cavity‐bearing trees are important nesting sites for many birds and mammals but have become rare due to anthropogenic modification of natural environments. Nest boxes are often used to compensate for the loss of these microhabitats. Nest boxes contain amounts of organic debris exploited by a variety of organisms, mainly insects. We studied the largely unexplored group of nest‐dwelling insects by rearing them from plant detritus and animal remains accumulated in nest boxes of six bird and two mammal species, distributed in forest, farmland and urban environments in Poland. We recorded 119 species representing eight insect orders. Nest substrates composed of plant detritus and animal remains supported similar insect species richness but differed significantly in terms of the insect community composition. Nests of Falco tinnunculus and Tyto alba and also Parus spp. and Strix aluco had very similar insect communities. The structural compositions of insect communities were also similar in nests of Parus spp. and Sturnus vulgaris, and of F. tinnunculus and S. aluco. Flies and earwigs were associated with nests of Parus spp. and Sciurus vulgaris and were more abundant in forests and urban environments, whereas wasps preferred S. aluco nests in forests. Our study shows that nest boxes may serve as replacement habitats for a variety of nest‐associated insects. Therefore, we suggest a more flexible approach to nest boxes maintenance and management, for example, less frequent cleaning or providing more than one nest box in a given place to enhance conservation of nest‐associated insects.

Landscape and microhabitat features determine small mammal abundance in forest patches in agricultural landscapes.

Intensification of agricultural landscapes represent a major threat for biodiversity conservation also affecting several ecosystem services. The natural and semi-natural remnants, available in the agricultural matrix, represent important sites for small mammals and rodents, which are fundamental for sustaining various ecosystem functions and trophic chains. We studied the populations of two small mammals (Apodemus agrarius, A. sylvaticus) to evaluate the effects of landscape and habitat features on species abundance along a gradient of agricultural landscape intensification. The study was performed in Friuli Venezia Giulia (north-eastern Italy) during 19 months, in 19 wood remnants. Species abundance was determined using Capture-Mark-Recapture (CMR) techniques. In the same plots, main ecological parameters of the habitat (at microhabitat and patch scale) and landscape were considered. Abundance of A. agrarius increased in landscapes with high extent of permanent crops (i.e., orchards and poplar plantations) and low content of undecomposed litter in the wood understory. Instead, A. sylvaticus, a more generalist species, showed an opposite, albeit less strong, relationship with the same variables. Both species were not affected by any landscape structural feature (e.g., patch shape, isolation). Our findings showed that microhabitat features and landscape composition rather than wood and landscape structure affect populations’ abundance and species interaction. The opposite response of the two study species was probably because of their specific ecological requirements. In this light, conservation management of agricultural landscapes should consider the ecological needs of species at both landscape and habitat levels, by rebalancing composition patterns in the context of ecological intensification, and promoting a sustainable forest patch management.

Biological richness of Gunung Slamet, Central Java, and the need for its protection

AbstractDesignating protected areas remains a core strategy in biodiversity conservation. Despite high endemism, montane forests across the island of Java are under-represented in Indonesia's protected area network. Here, we document the montane biodiversity of Gunung Slamet, an isolated volcano in Central Java, and provide evidence to support its increased protection. During September–December 2018, we surveyed multiple sites for birds, primates, terrestrial mammals, reptiles, amphibians and vegetation. Survey methods included transects, camera traps and targeted searches at six sites, at altitudes of 970–2,512 m. We used species distribution models for birds and mammals of conservation concern to identify priority areas for protection. We recorded 99 bird species (13 globally threatened), 15 mammals (five globally threatened) and 17 reptiles and amphibians (two endemic). Our species distribution models showed considerable cross-taxon congruence between important areas on Slamet's upper slopes, generally above 1,800 m. Particularly important were records of the endemic subspecies of the Endangered Javan laughingthrush Garrulax rufifrons slamatensis, not recorded in the wild since 1925, the Endangered Javan gibbon Hylobates moloch and Javan surili Presbytis comata, and the Vulnerable Javan lutung Trachypithecus auratus and Javan leopard Panthera pardus melas. Recent forest loss has been modest, at least 280 km2 of continuous forest remain above 800 m, and our surveys show that forest habitats are in good condition. However, the mountain is widely used by trappers and hunters. Given its importance for biodiversity conservation, we discuss different options for improving the protection status of Gunung Slamet, including designation as a National Park or Essential Ecosystem.

Habitat value of, and social attitudes towards, dead trees in Canberra’s urban forest

ABSTRACT Dead trees can occur throughout an urban forest and need to be managed. Standing dead trees that have been made ‘safe’ through regular inspection and the removal of unstable and decaying material are called ‘totem trees’ by Transport Canberra and City Services in Canberra, Australia. This paper is a pilot case study of totem trees in Canberra, employing an innovative mixed-methods approach, which includes silvicultural assessment, focal sampling, ad libitum sampling, in situ observation of evidence for fauna presence, and public questionnaires. It demonstrates that totem trees have significant habitat value because they provide perching, nesting, vocalisation, habitation and feeding sites for birds and arboreal mammals, as well as habitation and food for reptiles, insects and fungi. Totem trees with greater structural complexity appear to be preferred by fauna. The questionnaire findings, from park users and nearby park residents, indicate a generally positive attitude towards totem trees, with most participants perceiving them as valuable habitat for fauna and appreciating their aesthetic appeal. This highlights an important juxtaposition of management priorities: the need to balance structural complexity with providing safe trees. The findings of this study underscore the need to maintain and enlarge the totem tree population given their significant habitat value and social functions. Freestanding, structurally complex dead trees with numerous hollows, branches and bark should be prioritised for conservation. Additionally, the raising of public awareness is recommended to address any ongoing public uncertainty regarding the safety of totem trees.

Development of epithelial cholinergic chemosensory cells of the urethra and trachea of mice

Cholinergic chemosensory cells (CCC) are infrequent epithelial cells with immunosensor function, positioned in mucosal epithelia preferentially near body entry sites in mammals including man. Given their adaptive capacity in response to infection and their role in combatting pathogens, we here addressed the time points of their initial emergence as well as their postnatal development from first exposure to environmental microbiota (i.e., birth) to adulthood in urethra and trachea, utilizing choline acetyltransferase (ChAT)-eGFP reporter mice, mice with genetic deletion of MyD88, toll-like receptor-2 (TLR2), TLR4, TLR2/TLR4, and germ-free mice. Appearance of CCC differs between the investigated organs. CCC of the trachea emerge during embryonic development at E18 and expand further after birth. Urethral CCC show gender diversity and appear first at P6-P10 in male and at P11-P20 in female mice. Urethrae and tracheae of MyD88- and TLR-deficient mice showed significantly fewer CCC in all four investigated deficient strains, with the effect being most prominent in the urethra. In germ-free mice, however, CCC numbers were not reduced, indicating that TLR2/4-MyD88 signaling, but not vita-PAMPs, governs CCC development. Collectively, our data show a marked postnatal expansion of CCC populations with distinct organ-specific features, including the relative impact of TLR2/4-MyD88 signaling. Strong dependency on this pathway (urethra) correlates with absence of CCC at birth and gender-specific initial development and expansion dynamics, whereas moderate dependency (trachea) coincides with presence of first CCC at E18 and sex-independent further development.

Controversial epiglyptic thrust sheets: The case of the Daroca Thrust (Iberian Chain, Spain)

Epiglyptic thrusts can be misinterpreted as paleolandslides since they underwent displacement on the Earth surface. The Daroca Thrust has been object of controversial interpretations owing to (i) the particular style of its frontal structure (a thin slab of Cambrian dolostones overthrusting syntectonic Miocene deposits), and (ii) its relatively young age with respect to the overall compressional building of the Iberian chain. While several authors have interpreted its frontal flat as a synsedimentary landslide, a number of key features evince that it represents an epiglyptic thrust: (i) recumbent folds in competent Cambrian dolostones; (ii) thick damage zone with foliated fault rocks; (iii) physical continuity between the frontal flat and the main thrust ramp; (iv) transport directions towards NNE and E consistently recorded in both of them. Geometric reconstruction in cross section indicates that the syntectonic deposits of the Daroca area lie below the well-dated succession of the Aragonian stratotype (Middle Miocene). Nevertheless, by extrapolating the age model resulting from the complete succession of mammal sites, it can be inferred that the slip on the Daroca Thrust still took place during Middle Aragonian time.

3D in situ imaging of the female reproductive tract reveals molecular signatures of fertilizing spermatozoa in mice.

Out of millions of ejaculated sperm, a few reach the fertilization site in mammals. Flagellar Ca2+ signaling nanodomains, organized by multi-subunit CatSper calcium channel complexes, are pivotal for sperm migration in the female tract, implicating CatSper-dependent mechanisms in sperm selection. Here using biochemical and pharmacological studies, we demonstrate that CatSper1 is an O-linked glycosylated protein, undergoing capacitation-induced processing dependent on Ca2+ and phosphorylation cascades. CatSper1 processing correlates with protein tyrosine phosphorylation (pY) development in sperm cells capacitated in vitro and in vivo. Using 3D in situ molecular imaging and ANN-based automatic detection of sperm distributed along the cleared female tract, we demonstrate that spermatozoa past the utero-tubal junction possess the intact CatSper1 signals. Together, we reveal that fertilizing mouse spermatozoa in situ are characterized by intact CatSper channel, lack of pY, and reacted acrosomes. These findings provide molecular insight into sperm selection for successful fertilization in the female reproductive tract.

Overlapping den tree selection by three declining arboreal mammal species in an Australian tropical savanna.

Tree cavities are important denning sites for many arboreal mammals. Knowledge of cavity requirements of individual species, as well as potential den overlap among species, is integral to their conservation. In Australia’s tropical savannas, development of tree cavities is enhanced by high termite activity, and, conversely, reduced by frequent fires. However, it is poorly understood how the availability of tree cavities in the tropical savannas impacts tree cavity use and selection by cavity-dependent fauna. There has been a severe decline among arboreal mammal species in northern Australia over recent decades. Investigation of their cavity requirements may illuminate why these species have declined drastically in some areas but are persisting in others. Here we examined this issue in three species of arboreal mammals (Trichosurus vulpecula, Mesembriomys gouldii, Conilurus penicillatus) on Melville Island, northern Australia. We radiotracked individuals to their den sites to evaluate whether the species differ in their den tree and tree-cavity selection. The strongest influence on den tree selection was the presence of large cavities (> 10 cm entrance diameter), with all three species using larger cavities most frequently. Conilurus penicillatus, the smallest species, differed the most from the other species: it frequently was found in smaller, dead trees and its den sites were closer to the ground, including in hollow logs. The two larger species had broader den tree use, using larger live trees and dens higher up in the canopy. Dens of C. penicillatus are likely to be more susceptible to predation and destruction by high-intensity savanna fires. This may have contributed to this species’ rapid decline, both on Melville Island and on the mainland. However, the apparent preference for larger tree cavities by all three arboreal species is concerning due to the limited availability of large trees across Australian savannas, which are subject to frequent, high-intensity fires.

Incorporating hybrid models into lysine malonylation sites prediction on mammalian and plant proteins

Protein malonylation, a reversible post-translational modification of lysine residues, is associated with various biological functions, such as cellular regulation and pathogenesis. In proteomics, to improve our understanding of the mechanisms of malonylation at the molecular level,the identification of malonylation sites via an efficient methodology is essential. However, experimental identification of malonylated substrates via mass spectrometry is time-consuming, labor-intensive, and expensive. Although numerous methods have been developed to predict malonylation sites in mammalian proteins, the computational resource for identifying plant malonylation sites is very limited. In this study, a hybrid model incorporating multiple convolutional neural networks (CNNs) with physicochemical properties, evolutionary information,and sequenced-based features was developed for identifying protein malonylation sites in mammals. For plant malonylation, multiple CNNs and random forests were integrated into a secondary modeling phase using a support vector machine. The independent testing has demonstrated that the mammalian and plant malonylation models can yield the area under the receiver operating characteristic curves (AUC) at 0.943 and 0.772, respectively. The proposed scheme has been implemented as a web-based tool, Kmalo (https://fdblab.csie.ncu.edu.tw/kmalo/home.html), which can help facilitate the functional investigation of protein malonylation on mammals and plants.

Late Aragonian mammal sites of Cuesta del Rey (Duero Basin, Burgos, Spain)

The Cuesta del Rey mammal sites located on the NE border of the Duero Basin are of great importance with regard to understand the general biostratigraphy of the basin, because Miocene mammal sites are extremely scarce in this area in comparison with the central part of the basin. The mammals identified in Cuesta del Rey-1 are: Eulipotyphla: cf. Miosorex sp.; Rodentia: Heteroxerus sp., Armantomys cf. tricristatus, Megacricetodon ibericus, Megacricetodon minor-Megacricetodon debruijni, Hispanomys sp. and Democricetodon sp. The Cuesta del Rey-1 rodent assemblage is characteristic of the end of the upper Aragonian (MN 7/8, end of the middle Miocene), equivalent to the local subzone G3 of the G zone. The presence of the genera Heteroxerus and Armantomys, and the predominance of Megacricetodon (with 80% of the total percentage of the minimum number of individuals of the micromammals) suggested an open savannah or steppe palaeoenvironment. The mammals identified in Cuesta del Rey-3 are: Rodentia: Megacricetodon cf. ibericus; Artiodactyla: Dorcatherium sp. and Listriodon cf. splendens. Dorcatherium sp. represents the first appearance of the Tragulidae family in the Duero Basin, suggesting the existence of permanent watercourses.

Telocytes and lymphatic endothelial cells: Two immunophenotypically distinct and spatially close cell entities

Telocytes (TCs) have recently emerged as a peculiar type of stromal cells located in both perivascular and interstitial compartments of multiple anatomical sites in humans, other mammals and vertebrates. Pioneer electron microscopy studies have ultrastructurally defined TCs as “stromal cells with telopodes” (i.e. very long and thin cell processes with a moniliform morphology conferred by the irregular alternation of slender segments and small, bead-like, dilated portions), whereupon it has become apparent that TCs largely correspond to the CD34+ stromal/interstitial cells detectable by immunohistochemical assays. Besides CD34, TCs are also characterized by the expression of platelet-derived growth factor receptor (PDGFR)α. Interestingly, recent works recommended that lymphatic endothelial cell (LEC) markers should be routinely assessed to discriminate with certainty TCs from LECs, because these two cell types may exhibit similar morphological traits, especially when initial lymphatics are sectioned longitudinally and appear as vascular profiles with no obvious lumen. Furthermore, it has been argued that lymphatic microvessels immunostained for the small mucin-type transmembrane glycoprotein podoplanin (PDPN), which is widely used as lymphatic endothelial marker, can be easily misidentified as TCs. Nevertheless, surprisingly these assumptions were not based on double tissue immunostaining for TC and LEC markers. Therefore, the present morphological study was undertaken to precisely investigate the mutual spatial organization and putative relationships of TCs and lymphatic vessels in tissues from different human organs. For this purpose, we carried out a series of double immunofluorescence analyses simultaneously detecting the CD34 or PDGFRα antigen and a marker of LECs, either PDPN or lymphatic vessel endothelial hyaluronan receptor-1 (LYVE-1). In the connective tissue compartment of different organs, TCs were CD34+/PDGFRα+/PDPN−/LYVE-1− while LECs were CD34−/PDGFRα−/PDPN+/LYVE-1+, thus representing two definitely distinct, though spatially close, cell entities. The arrangement of telopodes to intimately surround the abluminal side of LECs suggests a possible role of TCs in the regulation of lymphatic capillary functionality, which is worth investigating further.

Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals

ABSTRACTIn the present study, we applied our ‘precise annotation’ to the mitochondrial (mt) genomes of human, chimpanzee, rhesus macaque and mouse using 5′ and 3′ end small RNAs. Our new annotations updated previous annotations. In particular, our new annotations led to two important novel findings: (1) the identification of five Conserved Sequence Blocks (CSB1, CSB2, CSB3, LSP and HSP) in the control regions; and (2) the annotation of Transcription Initiation and novel Transcription Termination Sites. Based on these annotations, we proposed a novel model of mt transcription which can account for the mt transcription and its regulation in mammals. According to our model, Transcription Termination Sites function as switches to regulate the production of short, long primary transcripts and uninterrupted transcription, rather than simply terminate the mt transcription. Moreover, the expression levels of mitochondrial transcription termination factors control the proportions of rRNAs, mRNAs and lncRNAs in total mt RNA. Our findings point to the existence of many other, as yet unidentified, Transcription Termination Sites in mammals.