bESC from cloned embryos do not retain transcriptomic or epigenetic memory from somatic donor cells

In brief

Epigenetic reprogramming after mammalian somatic cell nuclear transfer is often incomplete, resulting in low efficiency of cloning. However, gene expression and histone modification analysis indicated high similarities in transcriptome and epigenomes of bovine embryonic stem cells from in vitro fertilized and somatic cell nuclear transfer embryos.

Abstract

Embryonic stem cells (ESC) indefinitely maintain the pluripotent state of the blastocyst epiblast. Stem cells are invaluable for studying development and lineage commitment, and in livestock, they constitute a useful tool for genomic improvement and in vitro breeding programs. Although these cells have been recently derived from bovine blastocysts, a detailed characterization of their molecular state is lacking. Here, we apply cutting-edge technologies to analyze the transcriptomic and epigenomic landscape of bovine ESC (bESC) obtained from in vitro fertilized (IVF) and somatic cell nuclear transfer (SCNT) embryos. bESC were efficiently derived from SCNT and IVF embryos and expressed pluripotency markers while retaining genome stability. Transcriptome analysis revealed that only 46 genes were differentially expressed between IVF- and SCNT-derived bESC, which did not reflect significant deviation in cellular function. Interrogating histone 3 lysine 4 trimethylation, histone 3 lysine 9 trimethylation, and histone 3 lysine 27 trimethylation with cleavage under targets and tagmentation, we found that the epigenomes of both bESC groups were virtually indistinguishable. Minor epigenetic differences were randomly distributed throughout the genome and were not associated with differentially expressed or developmentally important genes. Finally, the categorization of genomic regions according to their combined histone mark signal demonstrated that all bESC shared the same epigenomic signatures, especially at gene promoters. Overall, we conclude that bESC derived from SCNT and IVF embryos are transcriptomically and epigenetically analogous, allowing for the production of an unlimited source of pluripotent cells from high genetic merit organisms without resorting to transgene-based techniques.

Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues

The use of Assay for Transposase-Accessible Chromatin (ATAC-seq) to profile chromatin accessibility has surged over the past years, but its applicability to tissues has been very limited. With the intent of preserving nuclear architecture during long-term storage, cryopreserved nuclei preparations from chicken lung were used to optimize ATAC-seq. Sequencing data were compared with existing DNase-seq, ChIP-seq, and RNA-seq data to evaluate library quality, ultimately resulting in a modified ATAC-seq method capable of generating high quality chromatin accessibility data from cryopreserved nuclei preparations. Using this method, nucleosome-free regions (NFR) identified in chicken lung overlapped half of DNase-I hypersensitive sites, coincided with active histone modifications, and specifically marked actively expressed genes. Notably, sequencing only the subnucleosomal fraction dramatically improved signal, while separation of subnucleosomal reads post-sequencing did not improve signal or peak calling. The broader applicability of this modified ATAC-seq technique was tested using cryopreserved nuclei preparations from pig tissues, resulting in NFR that were highly consistent among biological replicates. Furthermore, tissue-specific NFR were enriched for binding motifs of transcription factors related to tissue-specific functions, and marked genes functionally enriched for tissue-specific processes. Overall, these results provide insights into the optimization of ATAC-seq and a platform for profiling open chromatin in animal tissues.

Electron Microscopic Analysis of Silicate and Calcium Particles in Cigarette Smoke Tar

Scanning electron microscopy with energy dispersive x-ray spectroscopy (SEM-EDS) supplies information that is complementary to those data traditionally obtained using inductively coupled plasma-mass spectrometry for analysis of inorganic tobacco and tobacco smoke constituents. The SEM-EDS approach was used to identify select inorganic constituents of mainstream cigarette smoke "tar." The nature of SEM-EDS instrumentation makes it an ideal choice for microstructural analyses as it provides information relevant to inorganic constituents that could result from exposure to combusted tobacco products. Our analyses show that aluminum silicates, silica, and calcium compounds were common constituents of cigarette mainstream smoke "tar." Identifying inorganic tobacco smoke constituents is important because inhalation of fine inorganic particles could lead to inflammatory responses in the lung and systemic inflammatory responses. As cigarette smoking causes chronic inflammation in the respiratory tract, information on inorganic particulate in mainstream smoke informs efforts to determine causative agents associated with increased morbidity and mortality from tobacco use.

Electron Microscopic Analysis of Surface Inorganic Substances on Oral and Combustible Tobacco Products

Although quantitative trace toxic metal analyses have been performed on tobacco products, little has been published on inorganic particulate constituents on and inside the products. We analyzed these constituents using scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS). The nature of SEM-EDS instrumentation makes it an ideal choice for inorganic particulate analyses and yields relevant information to potential exposures during consumption of oral tobacco products, and possibly as a consequence of smoking. Aluminum silicates, silica and calcium compounds were common inorganic particulate constituents of tobacco products. Aluminum silicates and silica from soil were found on external leaf surfaces. Phytolithic silica, found in the lumen of the plant leaf, is of biogenic origin. Calcium oxalate was also apparently of biogenic origin. Small mineral deposits on tobacco could have health implications. Minerals found on the surfaces of smokeless tobacco products could possibly abrade the oral mucosa and contribute to the oral inflammatory responses observed with smokeless tobacco product use. If micron and sub-micron size calcium particles on cigarette filler were transported in mainstream smoke, they could potentially induce a pulmonary irritant inflammation when inhaled. The transport of aluminum silicate and silica in smoke could potentially also contribute to chronic inflammatory disease.

Human sexuality: an interdisciplinary program for health care professionals and the physically disabled

The central feature of a program in human sexuality for health care professionals and persons with physical disabilities developed at the Texas Institute for Rehabilitation and Research (TIRR) is a 2 1/2-day Sexual Attitude Reassessment (SAR) Workshop. Although the content of this Workshop has many features in common with ones used elsewhere, its organization, financing, and development are relatively unique. Based in a small, specialty hospital in the South, it is a low-budget, largely self-supporting program run by an extradepartmental, multidisciplinary staff. Evaluations of 12 workshops involving over 500 disabled and ablebodied participants are compared with similar data reported in the literature along with information (before and after the workshop) concerning the participants' attitudes, behavior, and satisfaction regarding various sexual activities. There were programmatic, institutional, and community problems unique to developing this program, but it has unusual potential for personal and staff development, intrainstitutional team building and broader community service.