A Genomic Link From Heart Failure to Atrial Fibrillation Risk: FOG2 Modulates a TBX5/GATA4-Dependent Atrial Gene Regulatory Network.

BACKGROUND: The relationship between heart failure (HF) and atrial fibrillation (AF) is clear, with up to half of patients with HF progressing to AF. The pathophysiological basis of AF in the context of HF is presumed to result from atrial remodeling. Upregulation of the transcription factor FOG2 (friend of GATA2; encoded by ZFPM2) is observed in human ventricles during HF and causes HF in mice. METHODS: FOG2 expression was assessed in human atria. The effect of adult-specific FOG2 overexpression in the mouse heart was evaluated by whole animal electrophysiology, in vivo organ electrophysiology, cellular electrophysiology, calcium flux, mouse genetic interactions, gene expression, and genomic function, including a novel approach for defining functional transcription factor interactions based on overlapping effects on enhancer noncoding transcription. RESULTS: FOG2 is significantly upregulated in the human atria during HF. Adult cardiomyocyte-specific FOG2 overexpression in mice caused primary spontaneous AF before the development of HF or atrial remodeling. FOG2 overexpression generated arrhythmia substrate and trigger in cardiomyocytes, including calcium cycling defects. We found that FOG2 repressed atrial gene expression promoted by TBX5. FOG2 bound a subset of GATA4 and TBX5 co-bound genomic locations, defining a shared atrial gene regulatory network. FOG2 repressed TBX5-dependent transcription from a subset of co-bound enhancers, including a conserved enhancer at the Atp2a2 locus. Atrial rhythm abnormalities in mice caused by Tbx5 haploinsufficiency were rescued by Zfpm2 haploinsufficiency. CONCLUSIONS: Transcriptional changes in the atria observed in human HF directly antagonize the atrial rhythm gene regulatory network, providing a genomic link between HF and AF risk independent of atrial remodeling.

Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors.

Analyzing single-cell transcriptomes promises to decipher the plasticity, heterogeneity, and rapid switches in developmental cellular state transitions. Such analyses require the identification of gene markers for semi-stable transition states. However, there are nontrivial challenges such as unexplainable stochasticity, variable population sizes, and alternative trajectory constructions. By advancing current tipping-point theory-based models with feature selection, network decomposition, accurate estimation of correlations, and optimization, we developed BioTIP to overcome these challenges. BioTIP identifies a small group of genes, called critical transition signal (CTS), to characterize regulated stochasticity during semi-stable transitions. Although methods rooted in different theories converged at the same transition events in two benchmark datasets, BioTIP is unique in inferring lineage-determining transcription factors governing critical transition. Applying BioTIP to mouse gastrulation data, we identify multiple CTSs from one dataset and validated their significance in another independent dataset. We detect the established regulator Etv2 whose expression change drives the haemato-endothelial bifurcation, and its targets together in CTS across three datasets. After comparing to three current methods using six datasets, we show that BioTIP is accurate, user-friendly, independent of pseudo-temporal trajectory, and captures significantly interconnected and reproducible CTSs. We expect BioTIP to provide great insight into dynamic regulations of lineage-determining factors.

Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq.

Long noncoding RNAs (lncRNAs) localize in the cell nucleus and influence gene expression through a variety of molecular mechanisms. Chromatin-enriched RNAs (cheRNAs) are a unique class of lncRNAs that are tightly bound to chromatin and putatively function to locally cis-activate gene transcription. CheRNAs can be identified by biochemical fractionation of nuclear RNA followed by RNA sequencing, but until now, a rigorous analytic pipeline for nuclear RNA-seq has been lacking. In this study, we survey four computational strategies for nuclear RNA-seq data analysis and develop a new pipeline, Tuxedo-ch, which outperforms other approaches. Tuxedo-ch assembles a more complete transcriptome and identifies cheRNA with higher accuracy than other approaches. We used Tuxedo-ch to analyze benchmark datasets of K562 cells and further characterize the genomic features of intergenic cheRNA (icheRNA) and their similarity to enhancer RNAs (eRNAs). We quantify the transcriptional correlation of icheRNA and adjacent genes and show that icheRNA is more positively associated with neighboring gene expression than eRNA or cap analysis of gene expression (CAGE) signals. We also explore two novel genomic associations of cheRNA, which indicate that cheRNAs may function to promote or repress gene expression in a context-dependent manner. IcheRNA loci with significant levels of H3K9me3 modifications are associated with active enhancers, consistent with the hypothesis that enhancers are derived from ancient mobile elements. In contrast, antisense cheRNA (as-cheRNA) may play a role in local gene repression, possibly through local RNA:DNA:DNA triple-helix formation.

CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs.

Motivation: Long intergenic noncoding RNAs (lincRNAs) have risen to prominence in cancer biology as new biomarkers of disease. Those lincRNAs transcribed from active cis-regulatory elements (enhancers) have provided mechanistic insight into cis-acting regulation; however, in the absence of an enhancer hallmark, computational prediction of cis-acting transcription of lincRNAs remains challenging. Here, we introduce a novel transcriptomic method: a cis-regulatory lincRNA-gene associating metric, termed 'CisPi'. CisPi quantifies the mutual information between lincRNAs and local gene expression regarding their response to perturbation, such as disease risk-dependence. To predict risk-dependent lincRNAs in neuroblastoma, an aggressive pediatric cancer, we advance this scoring scheme to measure lincRNAs that represent the minority of reads in RNA-Seq libraries by a novel side-by-side analytical pipeline. Results: Altered expression of lincRNAs that stratifies tumor risk is an informative readout of oncogenic enhancer activity. Our CisPi metric therefore provides a powerful computational model to identify enhancer-templated RNAs (eRNAs), eRNA-like lincRNAs, or active enhancers that regulate the expression of local genes. First, risk-dependent lincRNAs revealed active enhancers, over-represented neuroblastoma susceptibility loci, and uncovered novel clinical biomarkers. Second, the prioritized lincRNAs were significantly prognostic. Third, the predicted target genes further inherited the prognostic significance of these lincRNAs. In sum, RNA-Seq alone is sufficient to identify disease-associated lincRNAs using our methodologies, allowing broader applications to contexts in which enhancer hallmarks are not available or show limited sensitivity. Availability and implementation: The source code is available on request. The prioritized lincRNAs and their target genes are in the Supplementary Material. Supplementary information: Supplementary data are available at Bioinformatics online.

Microbial community responses reduce soil carbon loss in Tibetan alpine grasslands under short-term warming.

Changes in labile carbon (LC) pools and microbial communities are the primary factors controlling soil heterotrophic respiration (Rh ) in warming experiments. Warming is expected to initially increase Rh but studies show this increase may not be continuous or sustained. Specifically, LC and soil microbiome have been shown to contribute to the effect of extended warming on Rh . However, their relative contribution is unclear and this gap in knowledge causes considerable uncertainty in the prediction of carbon cycle feedbacks to climate change. In this study, we used a two-step incubation approach to reveal the relative contribution of LC limitation and soil microbial community responses in attenuating the effect that extended warming has on Rh . Soil samples from three Tibetan ecosystems-an alpine meadow (AM), alpine steppe (AS), and desert steppe (DS)-were exposed to a temperature gradient of 5-25°C. After an initial incubation period, soils were processed in one of two methods: (a) soils were sterilized then inoculated with parent soil microbes to assess the LC limitation effects, while controlling for microbial community responses; or (b) soil microbes from the incubations were used to inoculate sterilized parent soils to assess the microbial community effects, while controlling for LC limitation. We found both LC limitation and microbial community responses led to significant declines in Rh by 37% and 30%, respectively, but their relative contributions were ecosystem specific. LC limitation alone caused a greater Rh decrease for DS soils than AMs or ASs. Our study demonstrates that soil carbon loss due to Rh in Tibetan alpine soils-especially in copiotrophic soils-will be weakened by microbial community responses under short-term warming.

ETV2 primes hematoendothelial gene enhancers prior to hematoendothelial fate commitment.

Mechanisms underlying distinct specification, commitment, and differentiation phases of cell fate determination remain undefined due to difficulties capturing these processes. Here, we interrogate the activity of ETV2, a transcription factor necessary and sufficient for hematoendothelial differentiation, within isolated fate intermediates. We observe transcriptional upregulation of Etv2 and opening of ETV2-binding sites, indicating new ETV2 binding, in a common cardiac-hematoendothelial progenitor population. Accessible ETV2-binding sites are active at the Etv2 locus but not at other hematoendothelial regulator genes. Hematoendothelial commitment coincides with the activation of a small repertoire of previously accessible ETV2-binding sites at hematoendothelial regulators. Hematoendothelial differentiation accompanies activation of a large repertoire of new ETV2-binding sites and upregulation of hematopoietic and endothelial gene regulatory networks. This work distinguishes specification, commitment, and sublineage differentiation phases of ETV2-dependent transcription and suggests that the shift from ETV2 binding to ETV2-bound enhancer activation, not ETV2 binding to target enhancers, drives hematoendothelial fate commitment.

Enhanced spring temperature sensitivity of carbon emission links to earlier phenology.

Phenology has a great effect on the carbon cycle. Significant relationships have been well demonstrated between phenology and photosynthesis. However, few studies have been undertaken to characterize relationships between phenology and ecosystem respiration (Re). We conducted a reciprocal transplant experiment among three elevations for two-years to measure Re over six phenological sequences throughout the growing seasons. Our results showed that changes in phenological duration were mainly determined by the onset of phenology, as one day advance of phenological onset could lengthen 0.13 days of phenological duration. Advances in early spring phenophases (i.e., first leaf-out, first bud/boot-set and first flowering) under warming strengthened the temperature sensitivity of Re. However, the late phenophases (i.e., first seeding-set, first post-fruiting vegetation and first leaf-coloring) had non-significant relationships with Re. In total, after pooling all the data, one day advance of phenophases would increase Re by 2.23% under warming. In particular, Re would increase by 29.12% with an advance of phenophases by 8.46 days of under a 1.5 °C warming scenario. Our analysis of the coupling between temperature/moisture-phenology-Re may further supplement evidence that warmer spring temperature increases carbon emission by advancing early phenophases. This points to a faster and easier way to investigate how aboveground functional traits (phenology) affect unseen functional traits (Re) on the Tibetan Plateau.

Divergent Responses of Community Reproductive and Vegetative Phenology to Warming and Cooling: Asymmetry Versus Symmetry.

Few studies have focused on the response of plant community phenology to temperature change using manipulative experiments. A lack of understanding of whether responses of community reproductive and vegetative phenological sequences to warming and cooling are asymmetrical or symmetrical limits our capacity to predict responses under warming and cooling. A reciprocal transplant experiment was conducted for 3 years to evaluate response patterns of the temperature sensitivities of community phenological sequences to warming (transferred downward) and cooling (transferred upward) along four elevations on the Tibetan Plateau. We found that the temperature sensitivities of flowering stages had asymmetric responses to warming and cooling, whereas symmetric responses to warming and cooling were observed for the vegetative phenological sequences. Our findings showed that coverage changes of flowering functional groups (FFGs; i.e., early-spring FFG, mid-summer FFG, and late-autumn FFG) and their compensation effects combined with required accumulated soil temperatureto codetermined the asymmetric and symmetric responses of community phenological sequences to warming and cooling. These results suggest that coverage change in FFGs on warming and cooling processes can be a primary driver of community phenological variation and may lead to inaccurate phenlogical estimation at large scale, such as based on remote sensing.

Opposite effects of winter day and night temperature changes on early phenophases.

Changes in day (maximum temperature, TMAX ) and night temperature (minimum temperature, TMIN ) in the preseason (e.g., winter and spring) may have opposite effects on early phenophases (e.g., leafing and flowering) due to changing requirements of chilling accumulations (CAC) and heating accumulations (HAC), which could cause advance, delay or no change in early phenophases. However, their relative effects on phenology are largely unexplored, especially on the Tibetan Plateau. Here, observations were performed using a warming and cooling experiment in situ through reciprocal transplantation (2008-2010) on the Tibetan Plateau. We found that winter minimum temperature (TMIN ) warming significantly delayed mean early phenophases by 8.60 d/°C, but winter maximum temperature (TMAX ) warming advanced them by 12.06 d/°C across six common species. Thus, winter mean temperature warming resulted in a net advance of 3.46 d/°C in early phenophases. In contrast, winter TMIN cooling, on average, significantly advanced early phenophases by 5.12 d/°C, but winter TMAX cooling delayed them by 7.40 d/°C across six common species, resulting in a net delay of 2.28 d/°C for winter mean temperature cooling. The opposing effects of TMAX and TMIN warming on the early phenophases may be mainly caused by decreased CAC due to TMIN warming (5.29 times greater than TMAX ) and increased HAC due to TMAX warming (3.25 times greater than TMIN ), and similar processes apply to TMAX and TMIN cooling. Therefore, our study provides another insight into why some plant phenophases remain unchanged or delayed under climate change.