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Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs

Variable levels of DNA methylation have been reported at tissue-specific differential methylation regions (DMRs) overlapping enhancers, including super-enhancers (SEs) associated with key cell identity genes, but the mechanisms responsible for this intriguing behavior are not well understood. more »

Nature Methods logo

Joint profiling of DNA methylation and chromatin architecture in single cells

We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. more »

JCO precision oncology

Distinct DICER1 Hotspot Mutations Identify Bilateral Tumors as Separate Events

DICER1 syndrome1 predisposes to a variety of cancers, including pleuropulmonary blastoma (PPB),2 ovarian Sertoli-Leydig cell tumor (SLCT),3 embryonal rhabdomyosarcoma,4 and kidney tumors.58  ] more »

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

Abstract

The synthesis of pre-mRNA by RNA polymerase II (Pol II) involves the formation of a transcription initiation complex, and a transition to an elongation complex more »

Oxford University Press

Thirteen new plastid genomes from mixotrophic and autotrophic species provide insights into heterotrophy evolution in Neottieae orchids

Abstract

Mixotrophic species use both organic and mineral carbon sources. Some mixotrophic plants combine photosynthesis and a nutrition called mycoheterotrophy, where carbon is obtained from fungi forming mycorrhizal symbiosis with their roots. more »

science direct

Ancient DNA from a 2,500-year-old Caribbean fossil places an extinct bird (Caracara creightoni) in a phylogenetic context

Abstract

Since the late Pleistocene humans have caused the extinction of species across our planet. Placing these extinct species in the tree of life with genetic data is essential to understand the ecological and evolutionary implications of these losses. more »

BMC

Cut-C: cleavage under tethered nuclease for conformational capture

Abstract

Background
Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Existing methods, such as chromosome conformation capture (3C) and Hi-C have enabled the identification of novel aspects of chromatin structure. more »

BMC

Revealing the pathogenic changes of PAH based on multiomics characteristics

Abstract

Background

Pulmonary artery hypertension (PAH), which is characterized by an increase in pulmonary circulation blood pressure, is a fatal disease, and its pathogenesis remains unclear. more »

birth defects research

Exome sequencing of family trios from the National Birth Defects Prevention Study: Tapping into a rich resource of genetic and environmental data

Abstract

Background

The National Birth Defects Prevention Study (NBDPS) is a multisite, population‐based, case–control study of genetic and nongenetic risk factors for major structural birth defects. Eligible women had a pregnancy affected by a birth defect or a liveborn child without a birth defect between 1997 and 2011. more »

scientific-reports

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing

Whole genome bisulfite sequencing (WGBS), with its ability to interrogate methylation status at single CpG site resolution epigenome-wide, is a powerful technique for use in molecular experiments. Here, we aim to advance strategies for accurate and efficient WGBS for application in future large-scale epidemiological studies. more »

archives of Microbiology
Blastochloris tepida, sp. nov., a thermophilic species of the bacteriochlorophyll b-containing genus Blastochloris

A new taxon is created for the thermophilic purple nonsulfur bacterium previously designated as Rhodopseudomonas strain GI. Strain GI was isolated from a New Mexico (USA) hot spring microbial mat and grows optimally above 40 °C and to a maximum of 47 °C. Strain GI is a bacteriochlorophyll b-containing species of purple nonsulfur bacteria and displays a budding morphology, typical of species of the genus Blastochloris. more »

Nature Communications
Retention of paternal DNA methylome in the developing zebrafish germline

Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell (PGC) formation. However, it is currently unclear how evolutionarily conserved these processes are. more »

KoreaMed Synapse
Genomic analysis of Korean patients with advanced prostate cancer by use of a comprehensive next-generation sequencing panel and low-coverage, whole-genome sequencing

Prostate cancer (PCa) is the most common nonskin malignancy diagnosed in males globally [1]. More than one million patients are diagnosed with PCa yearly, and the mortality rate is estimated at over 300,000 annually [2]. more »

MD Edge ObGyn
Targeted sequencing panel IDs Lynch syndrome in women with/at risk for endometrial cancer

A targeted next-generation sequencing panel rapidly identifies both germline and somatic Lynch syndrome pathogenic mutations in women with – or at risk for – endometrial cancer, according to findings in a prospective patient cohort. more »

Optimizing de novo genome assembly from PCR-amplified metagenomes

Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated… more »

Use of a Targeted Lynch Syndrome Next Generation Sequencing Panel in Women at Risk for or With Endometrial Cancer [32M]

Women with endometrial cancer should be screened for Lynch syndrome (LS), a hereditary cancer syndrome caused by germline mutations in DNA mismatch repair (MMR) genes. This information directly affects immediate clinical management including future risk reducing/surveillance strategies for patients and at-risk family members. It is currently unclear how best to provide molecular screening… more »

Robust single-cell DNA methylome profiling with snmC-seq2

Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader applications of the method have been impeded by the modest quality of sequencing libraries. more »

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL

Cancer evolution is fueled by epigenetic as well as genetic diversity. In chronic lymphocytic leukemia (CLL), intra-tumoral DNA methylation (DNAme) heterogeneity empowers evolution. more »

Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study

Next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) supports blood-based genomic profiling but is not yet routinely implemented in the setting of a phase I trials clinic. more »

Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development

Studies in vertebrates have outlined conserved molecular control of definitive endoderm (END) development. However, recent work also shows that key molecular aspects of human END regulation differ even from rodents. more »

mRNA reprogramming of T8993G Leigh’s syndrome fibroblast cells to create induced pluripotent stem cell models for mitochondrial disorders

Early molecular and developmental events impacting many incurable mitochondrial disorders are not fully understood and require generation of relevant patient and disease-specific stem cell models. In this study, we focus on the ability of a non-viral and integration-free reprogramming method for deriving clinical-grade iPSCs specific to Leigh’s syndrome (LS), a fatal neurodegenerative mitochondrial disorder of infants. more »

The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight

What to expect after a year in space

Space is the final frontier for understanding how extreme environments affect human physiology. Following twin astronauts, one of which spent a year-long mission on the International Space Station, Garrett-Bakelman et al. examined molecular and physiological traits that may be affected by time in space (see the Perspective by Löbrich and Jeggo). more »

Read the study at sciencemag.org

Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation

Genome-wide association studies in obesity have identified a large number of non-coding loci located near genes expressed in the central nervous system. However, due to the difficulties in isolating and characterizing specific neuronal subpopulations, few obesity-associated single-nucleotide polymorphisms have been functionally characterized. more »

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. more »

Soil microbial responses to drought and exotic plants shift carbon metabolism

Significant gaps in our understanding of how global change drivers interact to affect the resistance and functioning of microbial communities hinders our ability to model ecosystem responses and feedbacks to co-occurring global stressors. more »

Unlocking a mechanism of lineage determination in the development of primary cancers using genomics.

Researchers are performing WGS and WES to identify immune cell cytokines that act on oncogenically transforming hepatocyctesand their epigenetic regulation.  more »

The highest peaking calling, sensitivity, and specificity values recorded for ChIP-Seq.

Seven methods designed for low input DNA/ChIP-seq sample preparation  (Accel-NGS 2S, Bowman-method, HTML-PCR, SeqPlex, DNA SMART, TELP, and ThruPLEX) were performed on five replicates of 1 ng and 0.1 ng input.  more »