Thoughts about SLC16A2, TSIX and XIST gene like sites in the human genome and a potential role in cellular chromosome counting

A quantum mechanical approach to random X chromosome inactivation

<abstract> <p>The X chromosome inactivation is an essential mechanism in mammals' development, that despite having been investigated for 60 years, many questions about its choice process have yet to be fully answered. Therefore, a theoretical model was proposed here for the first time in an attempt to explain this puzzling phenomenon through a quantum mechanical approach. Based on previous data, this work theoretically demonstrates how a shared delocalized proton at a key base pair position could explain the random, instantaneous, and mutually exclusive nature of the choice process in X chromosome inactivation. The main purpose of this work is to contribute to a comprehensive understanding of the X inactivation mechanism with a model proposal that can complement the existent ones, along with introducing a quantum mechanical approach that could be applied to other cell differentiation mechanisms.</p> </abstract>

Paircounting

X inactivation presents two longstanding puzzles: the counting and choice of X chromosomes. Here, we consider counting and choice in the context of pairing, both of the X and of the autosomes.

Assessing Skewed X-Chromosome Inactivation

We describe a simple and straightforward method for detection and characterization of X-chromosome inactivation in females and/or individuals with more than one X chromosome. The X-chromosome inactivation pattern is visualized on a single-cell level using 5-ethynyl-2-deoxyuridine (EdU) instead of the previously widely applied 5-bromo-2'-deoxyuridine (BUdR). The fluorochrome-labeled nucleoside analog EdU is incorporated into late-replication chromosomal regions of living blood cells in vitro; thus, it can also be used to specifically highlight the inactive X chromosome within a cytogenetic preparation. The EdU-based test for assessing skewed X-chromosome inactivation can only be meaningfully applied if the X chromosome of the index patient can be cytogenetically distinguished under a microscope from the normal one. © 2018 by John Wiley & Sons, Inc.

Parental origin of deletions and duplications - about the necessity to check for cryptic inversions

Background

Copy number variants (CNVs) are the genetic bases for microdeletion/ microduplication syndromes (MMSs). Couples with an affected child and desire to have further children are routinely tested for a potential parental origin of a specific CNV either by molecular karyotyping or by two color fluorescence in situ hybridization (FISH), yet. In the latter case a critical region probe (CRP) is combined with a control probe for identification of the chromosome in question. However, CNVs can arise also due to other reasons, like a recombination-event based on a submicroscopic, cryptic inversion in one of the parents.

Results

Seventy-four patients with different MMSs and overall 81 CNVs were studied here by a novel three color FISH approach. The way how three locus-specific probes are selected (one is the CRP and two are flanking it in a distance of 5-10 Mb) enables to detect or exclude two possible parental conditions as origins of the CNV seen in the index: (i) direct parental origin of the CNV (deletion or duplication) or (ii) a parental cryptic inversion. Thus, for overall 51/81 CNVs (63%) a parental origin could be determined. 36/51 (70.5%) inherited the CNV directly from one of the parents, but 15/51 (29.5%) were due to an exclusively by three color FISH detectable parental inversion. A 2:1 ratio of maternal versus paternal inheritance was found. Also almost two times more male than female were among the index patients.

Conclusion

The new, here suggested three color FISH approach is suited for more comprehensive parental studies of patients with MMS. The detection rate for parental origin was increased by 140% in this study. Still, for 30/81 cases (37%) no reason for the ‘de novo’ MMS in the affected index patient could be found by the here suggested FISH-probe set.

Electronic supplementary material

The online version of this article (10.1186/s13039-018-0369-1) contains supplementary material, which is available to authorized users.

X-autosome and X-Y Translocations in Female Carriers: X-chromosome Inactivation Easily Detectable by 5-ethynyl-2-deoxyuridine (EdU)

Here we report one new case each of an X-autosome translocation (maternally derived), and an X-Y-chromosome translocation. Besides characterizing the involved breakpoints and/or imbalances in detail by molecular cyto-genetics, also skewed X-chromosome inactivation was determined on single cell level using 5-ethynyl-2-deoxyuridine (EdU). Thus, we confirmed that the recently suggested EdU approach can be simply adapted for routine diagnostic use. The latter is important, as only by knowing the real pattern of the skewed X-chromosome inactivation, correct interpretation of obtained results and subsequent reliable genetic counseling, can be done.

The lncRNA n340790 accelerates carcinogenesis of thyroid cancer by regulating miR-1254

Long non-coding RNAs (lncRNAs) have been recently reported to be dysregulated and play a critical role in the progression of thyroid cancer. Here, we found that the lncRNA n340790 was highly expressed in human thyroid cancer tissues and was strongly correlated with the clinical characteristics of patients. There was a good prognostic value of n340790 for thyroid cancer. In vitro overexpression of n340790 promoted the development of thyroid cancer, while silencing n340790 inhibited this process. Additionally, n340790 accelerated the growth of thyroid cancer tumor in vivo. Furthermore, we discovered that n340790 could act as an endogenous sponge by directly binding to miR-1254 and downregulating miR-1254 expression. In addition, miR-1254 could inhibit the stimulatory effect of n340790 on the growth and invasion of thyroid cancer cells. In conclusion, n340790 promoted the development process of malignant thyroid cancer by regulating miR-1254, and targeting n340790 may be a promising strategy as a thyroid cancer therapy.

The long non-coding RNA NKILA inhibits the invasion-metastasis cascade of malignant melanoma via the regulation of NF-ĸB

The long non-coding RNA (lncRNA) NKILA has been reported to participate in the development of human cancers. The purpose of this study was to explore the potential role of lncRNA-NKILA, which acts through NF-ĸB, in the process of melanoma development. Real-time PCR (qRT-PCR) showed that NKILA was expressed at low levels in human melanoma tissues. The area under the ROC curve of NKILA was 0.875, which indicated that NKILA may be a potential diagnostic biomarker of melanoma. Our results also indicated that NKILA inhibited the progression of cell proliferation, migration, and invasion, and promoted apoptosis of melanoma cells. Furthermore, qRT-PCR showed that NF-κB, which was negatively correlated with NKILA, was highly expressed in human melanoma tissues. Moreover, our results indicated that NKILA inhibited the carcinogenesis of melanoma cells through the inhibition of NF-ĸB in vitro. More importantly, we found that NKILA suppressed the growth of melanoma tumors via NF-ĸB in vivo. In conclusion, NKILA suppressed the development of malignant melanoma via the regulation of NF-ĸB and may be a potential therapeutic target in patients with melanoma.