Localization of human SMC1 protein at kinetochores

Sex differences in the late first trimester human placenta transcriptome

Background

Development of the placenta during the late first trimester is critical to ensure normal growth and development of the fetus. Developmental differences in this window such as sex-specific variation are implicated in later placental disease states, yet gene expression at this time is poorly understood.

Methods

RNA-sequencing was performed to characterize the transcriptome of 39 first trimester human placentas using chorionic villi following genetic testing (17 females, 22 males). Gene enrichment analysis was performed to find enriched canonical pathways and gene ontologies in the first trimester. DESeq2 was used to find sexually dimorphic gene expression. Patient demographics were analyzed for sex differences in fetal weight at time of chorionic villus sampling and birth.

Results

RNA-sequencing analyses detected 14,250 expressed genes, with chromosome 19 contributing the greatest proportion (973/2852, 34.1% of chromosome 19 genes) and Y chromosome contributing the least (16/568, 2.8%). Several placenta-enriched genes as well as histone-coding genes were identified to be unique to the first trimester and common to both sexes. Further, we identified 58 genes with significantly different expression between males and females: 25 X-linked, 15 Y-linked, and 18 autosomal genes. Genes that escape X inactivation were highly represented (59.1%) among X-linked genes upregulated in females. Many genes differentially expressed by sex consisted of X/Y gene pairs, suggesting that dosage compensation plays a role in sex differences. These X/Y pairs had roles in parallel, ancient canonical pathways important for eukaryotic cell growth and survival: chromatin modification, transcription, splicing, and translation.

Conclusions

This study is the first characterization of the late first trimester placenta transcriptome, highlighting similarities and differences among the sexes in ongoing human pregnancies resulting in live births. Sexual dimorphism may contribute to pregnancy outcomes, including fetal growth and birth weight, which was seen in our cohort, with males significantly heavier than females at birth. This transcriptome provides a basis for development of early diagnostic tests of placental function that can indicate overall pregnancy heath, fetal-maternal health, and long-term adult health.

Electronic supplementary material

The online version of this article (10.1186/s13293-018-0165-y) contains supplementary material, which is available to authorized users.

Structural Maintenance of Chromosomes protein 1: Role in Genome Stability and Tumorigenesis

SMC1 (Structural Maintenance of Chromosomes protein 1), well known as one of the SMC superfamily members, has been explored to function in many activities including chromosome dynamics, cell cycle checkpoint, DNA damage repair and genome stability. Upon being properly assembled as part of cohesin, SMC1 can be phosphorylated by ATM and mediate downstream DNA damage repair after ionizing irradiation. Abnormal gene expression or mutation of SMC1 can cause defect in the DNA damage repair pathway, which has been strongly associated with tumorigenesis. Here we focus to discuss SMC1's role in genome stability maintenance and tumorigenesis. Deciphering the underlying molecular mechanism can provide insight into novel strategies for cancer treatment.

Meiotic chromosome pairing and bouquet formation during Eimeria tenella sporulation

In Eimeria tenella, meiotic division occurs exclusively in oocysts within the first 8h of sporulation. Difficulties with the wall-oocyst breakage in gaining access to chromosomes during meiosis have resulted in a scarcity of morphological data on Eimeria chromosomes. This study tracks the general behaviour of telomeres, attachment plaques and synaptonemal complexes in the nucleus of the meiotic oocyst of E. tenella. Fluorescence microscopy methods, in combination with immunoelectron microscopy techniques, were applied to obtain a series of time-lapse images during oocyst sporulation. Antibodies to Structural Maintenance of Chromosome proteins SMC1 and SMC3, and lamin were labelled with either fluorescence or colloidal gold to visualise the telomeres, central elements of the synaptonemal complex (SC) and nuclear periphery, respectively, at both the structural and ultrastructural levels. Using oocyst spreads and ultrathin sections of fixed oocysts it was possible to study telomere dynamics at stages during meiosis. The stages of the meiotic prophase I are delineated on the basis of the telomere position and the SC synapsis and desynapsis. During the leptotene stage, at 4h following the start of sporulation, meiotic chromosomes attached to the nuclear envelope. At that stage, chromosome synapsis was initiated in the telomeric regions but no interstitial synapsis pairing was observed. In the zygotene stage, telomere signals were clustered in a limited area of the nuclear envelope. Bouquet formation occurred at 5h after the start of sporulation, whereas chromosomes did not appear completely synapsed until the pachytene stage at 6h of sporulation. Desynapsis was observed at 8h of sporulation during the diplotene stage. This study provides the first morphological description of both the behaviour of the chromosomes and the timing of the prophase I stages in the meiotic nucleus of E. tenella.

Cohesin associates with spindle poles in a mitosis-specific manner and functions in spindle assembly in vertebrate cells

Cohesin is an essential protein complex required for sister chromatid cohesion. Cohesin associates with chromosomes and establishes sister chromatid cohesion during interphase. During metaphase, a small amount of cohesin remains at the chromosome-pairing domain, mainly at the centromeres, whereas the majority of cohesin resides in the cytoplasm, where its functions remain unclear. We describe the mitosis-specific recruitment of cohesin to the spindle poles through its association with centrosomes and interaction with nuclear mitotic apparatus protein (NuMA). Overexpression of NuMA enhances cohesin accumulation at spindle poles. Although transient cohesin depletion does not lead to visible impairment of normal spindle formation, recovery from nocodazole-induced spindle disruption was significantly impaired. Importantly, selective blocking of cohesin localization to centromeres, which disrupts centromeric sister chromatid cohesion, had no effect on this spindle reassembly process, clearly separating the roles of cohesin at kinetochores and spindle poles. In vitro, chromosome-independent spindle assembly using mitotic extracts was compromised by cohesin depletion, and it was rescued by addition of cohesin that was isolated from mitotic, but not S phase, cells. The combined results identify a novel spindle-associated role for human cohesin during mitosis, in addition to its function at the centromere/kinetochore regions.

Cohesin protein SMC1 is a centrosomal protein

Structural maintenance of chromosome protein 1 (SMC1) is well known for its roles in sister chromatid cohesion and DNA repair. In this study, we report a novel centrosomal localization of SMC1 within the cytoplasm in a variety of mammalian cell lines. We showed that SMC1 localized to centrosomes throughout the cell cycle in a microtubule-independent manner. Biochemically, SMC1 was cofractionated with the centrosomal protein gamma-tubulin in centrosomal preparation. Immunohistochemistry and immunoelectron microscopy performed on mouse tissue sections revealed that SMC1 antibody strongly labeled the base of cilia in ciliated epithelia, where basal bodies were located. Furthermore, we showed that SMC1 was associated with both centrioles of a centrosome at G0/G1 stage of the cell cycle. These results demonstrate that SMC1 is a centrosomal protein, suggesting possible involvement of SMC1 in centrosome/basal body-related functions, such as organization of dynamic arrays of microtubules and ciliary formation.

Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks

The biological interpretation of genetic interactions is a major challenge. Recently, Kelley and Ideker proposed a method to analyze together genetic and physical networks, which explains many of the known genetic interactions as linking different pathways in the physical network. Here, we extend this method and devise novel analytic tools for interpreting genetic interactions in a physical context. Applying these tools on a large-scale Saccharomyces cerevisiae data set, our analysis reveals 140 between-pathway models that explain 3765 genetic interactions, roughly doubling those that were previously explained. Model genes tend to have short mRNA half-lives and many phosphorylation sites, suggesting that their stringent regulation is linked to pathway redundancy. We also identify ‘pivot' proteins that have many physical interactions with both pathways in our models, and show that pivots tend to be essential and highly conserved. Our analysis of models and pivots sheds light on the organization of the cellular machinery as well as on the roles of individual proteins.

The role of X-linked genes in breast cancer

While contribution of X chromosome in the susceptibility of prostate and ovarian cancer has been demonstrated, the role of X-linked genes in breast carcinogenesis is not clearly known. This study investigated and compared the X-linked gene expression profiles of MMTV-c-myc transgenic mammary tumor (MT) or MMTV-c-myc/MT-tgf-alpha double transgenic mouse mammary tumor (DT) to lactating mammary gland. cDNA microarray analysis using the Affymetrix system identified 1081 genes localized on the X chromosome with 174 and 194 genes at +/-2-fold change levels in MT and DT samples, respectively. Differentially expressed X-linked genes were predominantly related to chromatin structure/remodeling (e.g., Hdac8, Suv39h1, RbAp46 and Adr1), segregation (e.g., CENP-I and smc111) and, ribosomal biogenesis and translational control (e.g., Dkc1, Rpl44, Rpl39, Eif2s3x, Gspt2 and Rsk4). Confirmation of microarray data by semi-quantitative and quantitative RT-PCR in selected X-linked genes also showed similar pattern. In addition, the expression pattern of two chromosomal regions, XE3 and XF5, suggests that XE3 may have escaped from inactivation and XF5 subjected to inactivation. In conclusion, our data suggest that X-linked genes may play the key regulatory roles in the maintenance of chromatin structure, accurate chromosomal segregation and translational control; hence deregulation of X-linked genes may promote mammary gland tumorigenesis by promoting genetic instability and cell proliferation. Increased understanding of the role of X-linked genes and genetic pathways will provide the strategies to develop the molecular therapeutics to treat and prevent reproductive related cancers.

Characterization ofArabidopsis thalianaSMC1 and SMC3: evidence that AtSMC3 may function beyond chromosome cohesion

Structural maintenance of chromosome (SMC) proteins are conserved in most prokaryotes and all eukaryotes examined. SMC proteins participate in many different aspects of chromosome folding and dynamics. They play essential roles in complexes that are responsible for sister chromatid cohesion, chromosome condensation and DNA repair. As part of studies to better understand SMC proteins and sister chromatid cohesion in plants we have characterized Arabidopsis SMC1 and SMC3. Although transcripts for AtSMC1 and AtSMC3 are present throughout the plant, transcript levels for the two genes vary between different tissues. Cell fractionation and immunolocalization results showed that AtSMC3 was present in the nucleus and cytoplasm. In the nucleus, it is primarily associated with the nuclear matrix during interphase and with chromatin from prophase through anaphase in both somatic and meiotic cells. During mitosis and meiosis the protein also co-localized with the spindle from metaphase to telophase. The distribution of AtSMC3 in syn1 mutant plants indicated that SYN1 is required for the proper binding of AtSMC3 to meiotic chromosomes, but not the spindle. Data presented here represent the first detailed cytological study of a plant SMC protein and suggest that SMC3 may have multiple functions in plants.

cDNA cloning and characterization of a novel gene encoding the MLF1-interacting protein MLF1IP

Myelodysplasia/acute myeloid leukemia (MDS/AML) is characterized by a t(3;5)(q25.1;q34) chromosomal translocation that forms a fusion gene between nucleophosmin (NPM) and MDS/myeloid leukemia factor 1 (MLF1). We identified a novel protein, MLF1-interacting protein (MLF1IP), that specifically associates with MLF1 by yeast two-hybrid analysis and in pulldown assays, and colocalizes with it in both the nuclei and cytoplasm of cells. The MLF1IP gene locus is at chromosome 4q35.1 and is composed of 14 exons spanning 75.8 kb of genomic DNA. The MLF1IP cDNA encodes a 46-kDa protein that contains two bipartite and two classical nuclear localization signals, two nuclear receptor-binding motifs (LXXLL), two leucine zippers, two PEST residues and several potential phosphorylation sites. MLF1IP transcripts are expressed in a variety of tissues (e.g. fetal liver, bone marrow, thymus and testis). MLF1IP appears to be a lineage-specific gene whose expression is confined exclusively to the CFU-E erythroid precursor cells, but not in mature erythrocytes. These observations, together with previous data demonstrating a role for MLF1 in suppressing red cell maturation, suggest a possible role for MLF1IP and MLF1 deregulation in the genesis of erythroleukemias.

Analysis of Scc1-deficient cells defines a key metaphase role of vertebrate cohesin in linking sister kinetochores

Cleavage of the cohesin subunit Scc1p/Mcd1p/Rad21 permits sister chromatid separation and is considered to trigger anaphase onset. It has also been suggested that the cohesin complex is essential for chromosome condensation and for assembling fully functional kinetochores. Here, we used vertebrate cells conditionally deficient in Scc1 to probe cohesin function in mitosis. Cells lacking cohesin arrest in prometaphase, with many chromosomes failing to align at a metaphase plate and high levels of the spindle assembly checkpoint protein, BubR1, at all kinetochores. We show that the structural integrity of chromosomes is normal in the absence of Scc1. Furthermore, specific inhibition of topoisomerase II, which is required for decatenation of replicated chromosomes, can bypass the cohesin requirement for metaphase chromosome alignment and spindle checkpoint silencing. Since the kinetochore effects of Scc1 deficiency can be compensated for by topoisomerase II inhibition, we conclude that Scc1 is not absolutely required for kinetochore assembly or function, and that its principal role in allowing the onset of anaphase is the establishment of sufficient inter-sister tension to allow biorientation.

SMC protein complexes and the maintenance of chromosome integrity

Structural maintenance of chromosomes (SMC) family proteins have attracted much attention for their unique protein structure and critical roles in mitotic chromosome organization. Elegant genetic and biochemical studies in yeast and Xenopus identified two different SMC heterodimers in two conserved multiprotein complexes termed 'condensin' and 'cohesin'. These complexes are required for mitotic chromosome condensation and sister chromatid cohesion, respectively, both of which are prerequisite to accurate segregation of chromosomes. Although structurally similar, the SMC proteins in condensin and cohesin appear to have distinct functions, whose specificity and cell cycle regulation are critically determined by their interactions with unique sets of associated proteins. Recent studies of subcellular localization of SMC proteins and SMC-containing complexes, identification of their interactions with other cellular factors, and discovery of new SMC family members have uncovered unexpected roles for SMC proteins and SMC-containing complexes in different aspects of genome functions and chromosome organization beyond mitosis, all of which are critical for the maintenance of chromosome integrity.