Widespread Expression of BORIS/CTCFL in Normal and Cancer Cells

BORIS (CTCFL) is the paralog of CTCF (CCCTC-binding factor; NM_006565), a ubiquitously expressed DNA-binding protein with diverse roles in gene expression and chromatin organisation. BORIS and CTCF have virtually identical zinc finger domains, yet display major differences in their respective C- and N-terminal regions. Unlike CTCF, BORIS expression has been reported only in the testis and certain malignancies, leading to its classification as a “cancer-testis” antigen. However, the expression pattern of BORIS is both a significant and unresolved question in the field of DNA binding proteins. Here, we identify BORIS in the cytoplasm and nucleus of a wide range of normal and cancer cells. We compare the localization of CTCF and BORIS in the nucleus and demonstrate enrichment of BORIS within the nucleolus, inside the nucleolin core structure and adjacent to fibrillarin in the dense fibrillar component. In contrast, CTCF is not enriched in the nucleolus. Live imaging of cells transiently transfected with GFP tagged BORIS confirmed the nucleolar accumulation of BORIS. While BORIS transcript levels are low compared to CTCF, its protein levels are readily detectable. These findings show that BORIS expression is more widespread than previously believed, and suggest a role for BORIS in nucleolar function

Epigenetic Patterns Maintained in Early Caenorhabditis elegans Embryos Can Be Established by Gene Activity in the Parental Germ Cells

Epigenetic information, such as parental imprints, can be transmitted with genetic information from parent to offspring through the germ line. Recent reports show that histone modifications can be transmitted through sperm as a component of this information transfer. How the information that is transferred is established in the parent and maintained in the offspring is poorly understood. We previously described a form of imprinted X inactivation in Caenorhabditis elegans where dimethylation on histone 3 at lysine 4 (H3K4me2), a mark of active chromatin, is excluded from the paternal X chromosome (Xp) during spermatogenesis and persists through early cell divisions in the embryo. Based on the observation that the Xp (unlike the maternal X or any autosome) is largely transcriptionally inactive in the paternal germ line, we hypothesized that transcriptional activity in the parent germ line may influence epigenetic information inherited by and maintained in the embryo. We report that chromatin modifications and histone variant patterns assembled in the germ line can be retained in mature gametes. Furthermore, despite extensive chromatin remodeling events at fertilization, the modification patterns arriving with the gametes are largely retained in the early embryo. Using transgenes, we observe that expression in the parental germline correlates with differential chromatin assembly that is replicated and maintained in the early embryo. Expression in the adult germ cells also correlates with more robust expression in the somatic lineages of the offspring. These results suggest that differential expression in the parental germ lines may provide a potential mechanism for the establishment of parent-of-origin epigenomic content. This content can be maintained and may heritably affect gene expression in the offspring

Evolution from XIST-Independent to XIST-Controlled X-Chromosome Inactivation: Epigenetic Modifications in Distantly Related Mammals

X chromosome inactivation (XCI) is the transcriptional silencing of one X in female mammals, balancing expression of X genes between females (XX) and males (XY). In placental mammals non-coding XIST RNA triggers silencing of one X (Xi) and recruits a characteristic suite of epigenetic modifications, including the histone mark H3K27me3. In marsupials, where XIST is missing, H3K27me3 association seems to have different degrees of stability, depending on cell-types and species. However, the complete suite of histone marks associated with the Xi and their stability throughout cell cycle remain a mystery, as does the evolution of an ancient mammal XCI system. Our extensive immunofluorescence analysis (using antibodies against specific histone modifications) in nuclei of mammals distantly related to human and mouse, revealed a general absence from the mammalian Xi territory of transcription machinery and histone modifications associated with active chromatin. Specific repressive modifications associated with XCI in human and mouse were also observed in elephant (a distantly related placental mammal), as was accumulation of XIST RNA. However, in two marsupial species the Xi either lacked these modifications (H4K20me1), or they were restricted to specific windows of the cell cycle (H3K27me3, H3K9me2). Surprisingly, the marsupial Xi was stably enriched for modifications associated with constitutive heterochromatin in all eukaryotes (H4K20me3, H3K9me3). We propose that marsupial XCI is comparable to a system that evolved in the common therian (marsupial and placental) ancestor. Silent chromatin of the early inactive X was exapted from neighbouring constitutive heterochromatin and, in early placental evolution, was augmented by the rise of XIST and the stable recruitment of specific histone modifications now classically associated with XCI

The evolution of the upright posture and gait—a review and a new synthesis

During the last century, approximately 30 hypotheses have been constructed to explain the evolution of the human upright posture and locomotion. The most important and recent ones are discussed here. Meanwhile, it has been established that all main hypotheses published until the last decade of the past century are outdated, at least with respect to some of their main ideas: Firstly, they were focused on only one cause for the evolution of bipedality, whereas the evolutionary process was much more complex. Secondly, they were all placed into a savannah scenario. During the 1990s, the fossil record allowed the reconstruction of emerging bipedalism more precisely in a forested habitat (e.g., as reported by Clarke and Tobias (Science 269:521–524, 1995) and WoldeGabriel et al. (Nature 412:175–178, 2001)). Moreover, the fossil remains revealed increasing evidence that this part of human evolution took place in a more humid environment than previously assumed. The Amphibian Generalist Theory, presented first in the year 2000, suggests that bipedalism began in a wooded habitat. The forests were not far from a shore, where our early ancestor, along with its arboreal habits, walked and waded in shallow water finding rich food with little investment. In contrast to all other theories, wading behaviour not only triggers an upright posture, but also forces the individual to maintain this position and to walk bipedally. So far, this is the only scenario suitable to overcome the considerable anatomical and functional threshold from quadrupedalism to bipedalism. This is consistent with paleoanthropological findings and with functional anatomy as well as with energetic calculations, and not least, with evolutionary psychology. The new synthesis presented here is able to harmonise many of the hitherto competing theories

Statistical and integrative system-level analysis of DNA methylation data

Epigenetics plays a key role in cellular development and function. Alterations to the epigenome are thought to capture and mediate the effects of genetic and environmental risk factors on complex disease. Currently, DNA methylation is the only epigenetic mark that can be measured reliably and genome-wide in large numbers of samples. This Review discusses some of the key statistical challenges and algorithms associated with drawing inferences from DNA methylation data, including cell-type heterogeneity, feature selection, reverse causation and system-level analyses that require integration with other data types such as gene expression, genotype, transcription factor binding and other epigenetic information

Grain Growth and Yield of Wheat as Influenced by Variety and Sowing Date

A field experiment was conducted at the Agronomy field, Sher-e-Bangla Agricultural University, Dhaka during November 2012 to April 2013 to evaluate the influence of variety and sowing date on grain growth and yield of wheat. The experiment consisted of four wheat variety viz., BARI Gom-21, BARI Gom-24, BARI Gom-25 and BARI Gom-26 and three sowing date viz., 20 November, 01December and 12 December. Grain growth, yield contributing characters and yield of wheat were significantly influenced by different variety and sowing date. Among the variety, BARI Gom-24 and BARI Gom-25 showed initial lower lag phase duration of 8 days after anthesis (DAA) and 12 DAA, respectively than BARI Gom-21 (16 DAA) sown at 01 December. The maximum grain growth rate whole over the period was maintained by BARI Gom-26 sown at 01 December. It reached peak at 20 DAA (1.17 mg /grain/day). The minimum growth rate was maintained by BARI Gom-21 and BARI Gom-24 sown at 12 December (0.15 mg /grain/day). BARI Gom-25 sown at 01December gave the highest yield (4.6 t ha−1) whereas BARI Gom-21 sown at 20 November gave the lowest (2.67 t ha−1). All the wheat varieties sown at 01 December yielded better than 20 November and 12 December sowing

Detecting arsenic-related skin lesions: experiences from a large community-based survey in Bangladesh.

A cross-sectional survey was conducted in Matlab, Bangladesh, to determine the prevalence of skin lesions (a three-step procedure) associated with arsenic exposure and discuss validity and feasibility in relation to recommended screening algorithms. Cases with skin lesions were identified by screening above 4 years of age (n = 166,934). Trained field teams conducted a careful house-to-house screening and identified 1682 individuals with skin lesions, who were referred to physicians for confirmation. Physicians diagnosed 579 cases as probable and documented all these with digital photographs. Two experts inspected all photographs for consensus agreement that was reached for 504 cases. Using the experts' opinions as reference, the positive predictive value of the physicians' diagnosis was 87% (male = 82% vs. female = 94%; p < 0.01). The physicians had difficulties in separating arsenic-induced keratosis from differential diagnoses, while probability for correct diagnosis was high for arsenic-related pigmentation changes. Including information on current arsenic concentration in drinking water (which was masked at time of skin examination) or urine in the diagnostic algorithm should have increased the number of false negative cases. In the present transition of drinking water sources these markers of current exposure levels provide no information on past exposure. A 2-3 step procedure with house-to-house screening and clinic-based confirmation of arsenic-induced skin lesions is a feasible approach. Information on arsenic concentration in current water sources or in urine should not have improved the precision in the diagnosis. These results may have policy implications for community screening of arsenic-related skin lesions in Bangladesh and elsewhere