Ultraconserved Enhancers Are Required for Normal Development.

Non-coding "ultraconserved" regions containing hundreds of consecutive bases of perfect sequence conservation across mammalian genomes can function as distant-acting enhancers. However, initial deletion studies in mice revealed that loss of such extraordinarily constrained sequences had no immediate impact on viability. Here, we show that ultraconserved enhancers are required for normal development. Focusing on some of the longest ultraconserved sites genome wide, located near the essential neuronal transcription factor Arx, we used genome editing to create an expanded series of knockout mice lacking individual or combinations of ultraconserved enhancers. Mice with single or pairwise deletions of ultraconserved enhancers were viable and fertile but in nearly all cases showed neurological or growth abnormalities, including substantial alterations of neuron populations and structural brain defects. Our results demonstrate the functional importance of ultraconserved enhancers and indicate that remarkably strong sequence conservation likely results from fitness deficits that appear subtle in a laboratory setting.

An atlas of dynamic chromatin landscapes in mouse fetal development.

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP-seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC-seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.

Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Enhancer redundancy provides phenotypic robustness in mammalian development.

Distant-acting tissue-specific enhancers, which regulate gene expression, vastly outnumber protein-coding genes in mammalian genomes, but the functional importance of this regulatory complexity remains unclear. Here we show that the pervasive presence of multiple enhancers with similar activities near the same gene confers phenotypic robustness to loss-of-function mutations in individual enhancers. We used genome editing to create 23 mouse deletion lines and inter-crosses, including both single and combinatorial enhancer deletions at seven distinct loci required for limb development. Unexpectedly, none of the ten deletions of individual enhancers caused noticeable changes in limb morphology. By contrast, the removal of pairs of limb enhancers near the same gene resulted in discernible phenotypes, indicating that enhancers function redundantly in establishing normal morphology. In a genetic background sensitized by reduced baseline expression of the target gene, even single enhancer deletions caused limb abnormalities, suggesting that functional redundancy is conferred by additive effects of enhancers on gene expression levels. A genome-wide analysis integrating epigenomic and transcriptomic data from 29 developmental mouse tissues revealed that mammalian genes are very commonly associated with multiple enhancers that have similar spatiotemporal activity. Systematic exploration of three representative developmental structures (limb, brain and heart) uncovered more than one thousand cases in which five or more enhancers with redundant activity patterns were found near the same gene. Together, our data indicate that enhancer redundancy is a remarkably widespread feature of mammalian genomes that provides an effective regulatory buffer to prevent deleterious phenotypic consequences upon the loss of individual enhancers.

Intracytoplasmic sperm injection versus conventional in-vitro fertilisation in couples with infertility in whom the male partner has normal total sperm count and motility: an open-label, randomised controlled trial.

BACKGROUND: The use of intracytoplasmic sperm injection has increased substantially worldwide, primarily in couples with non-male factor infertility. However, there is a paucity of evidence from randomised trials supporting this approach compared with conventional in-vitro fertilisation (IVF). We aimed to investigate whether intracytoplasmic sperm injection would result in a higher livebirth rate compared with conventional IVF. METHODS: This open-label, multicentre, randomised trial was done at two IVF centres in Ho Chi Minh City, Vietnam (IVFMD, My Duc Hospital and IVFAS, An Sinh Hospital). Eligible couples were aged at least 18 years and the male partner's sperm count and motility (progressive motility) were normal based on WHO 2010 criteria. Couples had to have undergone two or fewer previous conventional IVF or intracytoplasmic sperm injection attempts, have used an antagonist protocol for ovarian stimulation, and agree to have two or fewer embryos transferred. Couples were randomly assigned (1:1) to undergo either intracytoplasmic sperm injection or conventional IVF, using block randomisation with variable block size of 2, 4, or 8 and a telephone-based central randomisation method. The computer-generated randomisation list was prepared by an independent statistician who had no other involvement in the study. Embryologists and couples were not masked to study groups because of the type of interventions and differences in hospital fees, but clinicians performing embryo transfer were unaware of study group allocation. The primary outcome was livebirth after the first embryo transfer from the initiated cycle. Analyses were done on an intention-to-treat basis. The trial is registered with ClinicalTrials.gov, NCT03428919. FINDINGS: Between March 16, 2018, and Aug 12, 2019, we randomly assigned 1064 couples to intracytoplasmic sperm injection (n=532) or conventional IVF (n=532). Livebirth after the first embryo transfer from the initiated cycle occurred in 184 (35%) of 532 couples randomly assigned to intracytoplasmic sperm injection and in 166 (31%) of 532 couples randomly assigned to conventional IVF (absolute difference 3·4%, 95% CI -2·4 to 9·2; risk ratio [RR] 1·11, 95% CI 0·93 to 1·32; p=0·27). 29 (5%) couples in the intracytoplasmic sperm injection group and 34 (6%) couples in the conventional IVF group had fertilisation failure (absolute difference -0·9%, -4·0 to 2·1, RR 0·85, 95% CI 0·53 to 1·38; p=0·60). INTERPRETATION: In couples with infertility in whom the male partner has a normal total sperm count and motility, intracytoplasmic sperm injection did not improve the livebirth rate compared with conventional IVF. Our results challenge the value of the routine use of intracytoplasmic sperm injection in assisted reproduction techniques for this population. FUNDING: My Duc Hospital and Merck Sharp and Dohme.

Reference Intervals of Thyroid Function Tests in First Trimester Vietnamese Pregnant Women.

BACKGROUND: Although TSH suppression by elevated ß-hCG is essentially seen during first trimester, differences in TSH reference ranges between various countries have been reported. Physiologic changes during pregnancy may also influence FT4 assays. This study aims to establish method-specific reference intervals (RIs) of TSH, FT4, and FT3 in Vietnamese, first trimester pregnant women. METHODS: This cross-sectional study was conducted at My Duc Hospital, Ho Chi Minh, Vietnam. Women with singleton pregnancies in the first trimester and conceived naturally were included. Those with a history of thyroid disease, positive thyroid-specific autoantibodies, diffuse goiter or one thyroid nodule > 10 mm in size or ≥ 2 nodules detected by ultrasound, and taking medications affecting thyroid function were excluded. Serum TSH, FT4, and FT3 were measured by chemiluminescent detection technology on the Access 2 Immunoassay System (Beckman Coulter, Inc., USA). Intra- and interassay coefficients of variations (CV) were 3.6% and 4.4% for TSH, 5.4% and 6.1% for FT4, 6.6%, and 6.0% for FT3, respectively. The 2.5th and 97.5th percentiles were used to determine RIs. RESULTS: Between August 1, 2017, to December 1, 2018, there were 876 pregnant women who fulfilled inclusion and exclusion criteria. They had a mean age of 30.1 years, an average BMI of 21.3 kg/m2, and 77.3% of them were primigravida. The RIs for TSH, FT4 and FT3 were 0.17 - 2.35 mIU/L, 0.67 - 1.11 ng/dL and 2.82 - 3.90 pg/mL, respectively. CONCLUSIONS: Established RIs for TSH, FT4, and FT3 in Vietnamese women would help to reduce the misdiagnosis of gestational thyroid disorders.

The effectiveness of Paraffin oil and Mineral oil for day-5 embryo culture in couples undergoing in vitro fertilisation.

OBJECTIVE: This study evaluated the effectiveness of Paraffin oil versus Mineral oil for day-5 embryo culture in couples undergoing assisted reproductive technology (ART). METHODS: We performed a multi-centre, retrospective cohort study at IVFMD (My Duc Hospital) and IVFMD Phu Nhuan (My Duc Phu Nhuan Hospital) from January 2019 to September 2019. We studied couples treated by intracytoplasmic sperm injection (ICSI), using fresh, ejaculated semen and undergoing day-5 embryo transfer. Couples who underwent in vitro maturation (IVM) or oocyte donation cycles or couples where the woman had uterine abnormalities were excluded. From January 2019 to May 2019, we used Mineral oil (LiteOil, LifeGlobal) while Paraffin oil (Liquid Paraffin, Origio) was used from June 2019 to September 2019. The primary outcome was live birth rate after the first transfer, either from a fresh transfer or frozen embryo transfer. RESULTS: Between 1st January 2019 to 30th September 2019, there were 2,312 couples undergoing ART in both centres, of which 762 (377 in the Paraffin group and 385 in the Mineral group) eligible couples were included in the study. Baseline characteristics of couples were comparable between the two groups, with mean female age 31.5 ± 4.3 versus 31.9 ± 4.7 in the Paraffin and Mineral group. Live birth after the first transfer occurred in 153 (40.6%) couples in the Paraffin group, compared to 152 (39.5%) couples in the Mineral group (risk ratio 1.02, 95% confidence interval 0.91 - 1.14). Other secondary outcomes were comparable between the two groups. CONCLUSION: In day-5 embryo culture, Paraffin and Mineral oil resulted in a comparable live birth rate.

Genome-wide fetalization of enhancer architecture in heart disease.

Heart disease is associated with re-expression of key transcription factors normally active only during prenatal development of the heart. However, the impact of this reactivation on the regulatory landscape in heart disease is unclear. Here, we use RNA-seq and ChIP-seq targeting a histone modification associated with active transcriptional enhancers to generate genome-wide enhancer maps from left ventricle tissue from up to 26 healthy controls, 18 individuals with idiopathic dilated cardiomyopathy (DCM), and five fetal hearts. Healthy individuals have a highly reproducible epigenomic landscape, consisting of more than 33,000 predicted heart enhancers. In contrast, we observe reproducible disease-associated changes in activity at 6,850 predicted heart enhancers. Combined analysis of adult and fetal samples reveals that the heart disease epigenome and transcriptome both acquire fetal-like characteristics, with 3,400 individual enhancers sharing fetal regulatory properties. We also provide a comprehensive data resource (http://heart.lbl.gov) for the mechanistic exploration of DCM etiology.

Ultraconserved enhancer function does not require perfect sequence conservation.

Ultraconserved enhancer sequences show perfect conservation between human and rodent genomes, suggesting that their functions are highly sensitive to mutation. However, current models of enhancer function do not sufficiently explain this extreme evolutionary constraint. We subjected 23 ultraconserved enhancers to different levels of mutagenesis, collectively introducing 1,547 mutations, and examined their activities in transgenic mouse reporter assays. Overall, we find that the regulatory properties of ultraconserved enhancers are robust to mutation. Upon mutagenesis, nearly all (19/23, 83%) still functioned as enhancers at one developmental stage, as did most of those tested again later in development (5/9, 56%). Replacement of endogenous enhancers with mutated alleles in mice corroborated results of transgenic assays, including the functional resilience of ultraconserved enhancers to mutation. Our findings show that the currently known activities of ultraconserved enhancers do not necessarily require the perfect conservation observed in evolution and suggest that additional regulatory or other functions contribute to their sequence constraint.

Modification of Lignocellulosic Materials with a Mixture of m-DMDHEU/Choline Chloride to Remove CrO4 2-, NO3 -, and H2AsO4 - in Aqueous Solution.

A new denaturation agent is the mixture of 4,5-dihydroxy-1,3-bis(methoxymethyl)imidazolidin-2-one (m-DMDHEU)/choline chloride (CC) introduced to modify three kinds of lignocellulosic materials containing different lignin contents in the following order: cotton used in medicine < sawdust from acacia auriculiformis wood < powder from the coconut shell. The modification process is carried out through two main steps: 0.2 N NaOH solution with 70% v/v ethanol and 30% v/v water was applied to remove lignin and activate the initial raw materials, and then delignified materials were modified with m-DMDHEU/CC by using a parched heat supply method after chemical impregnation. Structural characterictics and physicochemical properties of modified materials were tested and dissected by scanning electron microscopy, Fourier transform infrared spectroscopy, solid-state 13C nuclear magnetic resonance spectroscopy (solid-state 13C CP-MAS NMR), specific surface area, and pH at the point of zero charge (pHPZC). The ability to adsorb and exchange anions of modified materials was referred and examined by using aqueous solutions containing CrO4 2-, NO3 -, and H2AsO4 - anions in different conditions. The results revealed that anionite lignocellulosic materials could separate these anions with very good efficiency and better than strong anion exchange resin (GA-13) in the same conditions; outlet water could meet the permissible drinking and living water standards; and the m-DMDHEU cross-link bridge also was a good bridge to connect CC to cellulose chain beside other common urea cross-link bridges.