Allele specific binding of histone modifications and a transcription factor does not predict allele specific expression in correlated ChIP-seq peak-exon pairs.

Allele specific expression (ASE) is widespread in many species including cows. Therefore, regulatory regions which control gene expression should show cis-regulatory variation which mirrors this differential expression within the animal. ChIP-seq peaks for histone modifications and transcription factors measure activity at functional regions and the height of some peaks have been shown to correlate across tissues with the expression of particular genes, suggesting these peaks are putative regulatory regions. In this study we identified ASE in the bovine genome in multiple tissues and investigated whether ChIP-seq peaks for four histone modifications and the transcription factor CTCF show allele specific binding (ASB) differences in the same tissues. We then investigate whether peak height and gene expression, which correlates across tissues, also correlates within the animal by investigating whether the direction of ASB in putative regulatory regions, mirrors that of the ASE in the genes they are putatively regulating. We found that ASE and ASB were widespread in the bovine genome but vary in extent between tissues. However, even when the height of a peak was positively correlated across tissues with expression of an exon, ASE of the exon and ASB of the peak were in the same direction only half the time. A likely explanation for this finding is that the correlations between peak height and exon expression do not indicate that the height of the peak causes the extent of exon expression, at least in some cases.

Dairy Cows Offered Fresh Chicory Instead of Ensiled Pasture during an Acute Heat Challenge Produced More Milk and Had Lower Body Temperatures.

The frequency, duration, and intensity of heat waves in Australia are increasing. To reduce the impact of heat waves on milk production, novel management strategies are required. Altering the forage type and amount offered affect the heat load on dairy cows and offer potential strategies to ameliorate the effects of hot weather. Thirty-two multiparous, lactating Holstein-Friesian cows were assigned one of four dietary treatments: chicory high amount, chicory low amount, pasture silage high amount, or pasture silage low amount. These cows were exposed to a heat wave in controlled-environment chambers. Cows that were offered fresh chicory had similar feed intake to cows that were offered pasture silage (15.3 kg DM/d). However, cows that were offered chicory produced greater energy-corrected milk (21.9 vs. 17.2 kg/d) and had a lower maximum body temperature (39.4 vs. 39.6 °C) than cows that were offered pasture silage overall. Cows that were offered the high amount of forage had greater feed intake (16.5 vs. 14.1 kg DM/d) and energy corrected milk yield (20.0 vs. 17.9 kg/d) than cows that were offered the low amount, as intended, but with no difference in maximum body temperature (39.5 °C). We conclude that feeding chicory instead of pasture silage to dairy cows shows promise as a dietary strategy to ameliorate the effect of heat exposure, and there was no advantage in restricting feed amount.

Effects of Heat Stress in Dairy Cows Offered Diets Containing Either Wheat or Corn Grain during Late Lactation.

Cereal grains that differ in the rate and extent of ruminal fermentation differ in heat increment and may be used to improve thermoregulation during heat stress. This experiment investigated the responses of dairy cows in late lactation to a heat challenge when offered wheat-grain or corn-grain. Eighteen lactating cows, 220 ± 94 (mean ± standard deviation) days in milk, 3.7 ± 0.17 years of age and 558 ± 37 kg bodyweight, were allocated treatments containing 6 kg dry matter (DM)/day of wheat grain or 6 kg DM/day corn grain (9 per treatment) plus 14 kg DM/day of alfalfa hay. Measurements were made during a 7-day pre-challenge period at ambient conditions in individual stalls, during a 4-day heat challenge (temperature humidity index of 74 to 84) in individual controlled-climate chambers, then during a 7-day recovery period at ambient conditions in individual stalls. During the heat challenge, cows offered corn had lower respiration rates (p = 0.017) and greater feed intake (p = 0.021) but energy-corrected milk (p = 0.097) was not different to that of cows offered wheat. Feeding corn grain to dairy cows during a heat challenge reduced some of the negative impacts of heat stress, enabling the cows to consume more forage compared with supplementing with wheat grain.

Dietary Fat and Betaine Supplements Offered to Lactating Cows Affect Dry Matter Intake, Milk Production and Body Temperature Responses to an Acute Heat Challenge.

Supplementing the diet of lactating cows with ingredients that increase energy density, or reduce internal heat production, may reduce some of the negative impacts of hot weather on milk yield. Thirty-two dairy cows were assigned either: (1) basal diet only, (2) basal diet plus canola oil, (3) basal diet plus betaine, or (4) basal diet plus canola oil and betaine. The basal diet was lucerne hay, pasture silage, and grain. Cows were exposed to a four-day heat challenge (temperature-humidity index 74 to 84) in controlled-environment chambers. Canola oil supplementation increased milk production (22.0 vs. 18.7 kg/d) across all periods of our experiment and increased body temperature (39.6 vs. 39.0 °C) during the heat challenge. Betaine supplementation reduced maximum body temperature during the pre-challenge period (39.2 vs. 39.6 °C) but not during the heat challenge (40.3 °C). Cows fed canola oil had greater declines in dry matter intake (5.4 vs 2.7 kg DM) and energy corrected milk (1.3 vs. 1.0 kg) from the pre-challenge to the heat challenge than other cows. Contrary to our expectations, the combination of fat and betaine supplements did not result in a clear benefit in terms of milk production or body temperature. Further work is warranted to understand the interactions between diet and hot weather.

Corrigendum: Putative Causal Variants Are Enriched in Annotated Functional Regions From Six Bovine Tissues.

[This corrects the article DOI: 10.3389/fgene.2021.664379.].

Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus.

To further the understanding of the evolution of transcriptional regulation, we profiled genome-wide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago. Evolutionary and developmental-stage differences in TSSs were detected across the sub-species, including translocation of dominant TSS and changes in TSS distribution. The 16% of all SNPs located in significant differentially used TSS clusters across sub-species had significant shifts in allele frequency (472 SNPs), indicating they may have been subject to selection. In spleen and muscle, a higher relative TSS expression was observed in Bos indicus than Bos taurus for all heat shock protein genes, which may be responsible for the tropical adaptation of Bos indicus.

Putative Causal Variants Are Enriched in Annotated Functional Regions From Six Bovine Tissues.

Genetic variants which affect complex traits (causal variants) are thought to be found in functional regions of the genome. Identifying causal variants would be useful for predicting complex trait phenotypes in dairy cows, however, functional regions are poorly annotated in the bovine genome. Functional regions can be identified on a genome-wide scale by assaying for post-translational modifications to histone proteins (histone modifications) and proteins interacting with the genome (e.g., transcription factors) using a method called Chromatin immunoprecipitation followed by sequencing (ChIP-seq). In this study ChIP-seq was performed to find functional regions in the bovine genome by assaying for four histone modifications (H3K4Me1, H3K4Me3, H3K27ac, and H3K27Me3) and one transcription factor (CTCF) in 6 tissues (heart, kidney, liver, lung, mammary and spleen) from 2 to 3 lactating dairy cows. Eighty-six ChIP-seq samples were generated in this study, identifying millions of functional regions in the bovine genome. Combinations of histone modifications and CTCF were found using ChromHMM and annotated by comparing with active and inactive genes across the genome. Functional marks differed between tissues highlighting areas which might be particularly important to tissue-specific regulation. Supporting the cis-regulatory role of functional regions, the read counts in some ChIP peaks correlated with nearby gene expression. The functional regions identified in this study were enriched for putative causal variants as seen in other species. Interestingly, regions which correlated with gene expression were particularly enriched for potential causal variants. This supports the hypothesis that complex traits are regulated by variants that alter gene expression. This study provides one of the largest ChIP-seq annotation resources in cattle including, for the first time, in the mammary gland of lactating cows. By linking regulatory regions to expression QTL and trait QTL we demonstrate a new strategy for identifying causal variants in cattle.

Measurement of Enteric Methane Emissions by the SF6 Technique Is Not Affected by Ambient Weather Conditions.

Despite the fact that the sulphur hexafluoride (SF6) tracer technique was developed over 25 years ago to measure methane production from grazing and non-housed animals, no studies have specifically investigated whether ambient wind speed, temperature, relative humidity and rainfall influence the accuracy of the method. The aim of this research was to investigate how these weather factors influence the measurement of enteric methane production by the SF6 technique. Six different cohorts of dairy cows (40 per cohort) were kept outdoors and fed a common diet during spring in 3 consecutive years. Methane production from individual cows was measured daily over the last 5 days of each 32-day period. An automated weather station measured air temperature, wind speed, relative humidity and rainfall every 10 min. Regression analyses were used to relate the average daily wind speed, average daily temperature, average daily relative humidity and total daily rainfall measurements to dry matter intake, average daily methane production and methane yield of each cohort of cows. It was concluded that the modified SF6 technique can be used outdoors during a range of wind speeds, ambient temperatures, relative humidities and rainfall conditions without causing a significant effect on the measurement of methane production or methane yield of dairy cows.

Expression of mitochondrial protein genes encoded by nuclear and mitochondrial genomes correlate with energy metabolism in dairy cattle.

BACKGROUND: Mutations in the mitochondrial genome have been implicated in mitochondrial disease, often characterized by impaired cellular energy metabolism. Cellular energy metabolism in mitochondria involves mitochondrial proteins (MP) from both the nuclear (NuMP) and mitochondrial (MtMP) genomes. The expression of MP genes in tissues may be tissue specific to meet varying specific energy demands across the tissues. Currently, the characteristics of MP gene expression in tissues of dairy cattle are not well understood. In this study, we profile the expression of MP genes in 29 adult and six foetal tissues in dairy cattle using RNA sequencing and gene expression analyses: particularly differential gene expression and co-expression network analyses. RESULTS: MP genes were differentially expressed (DE; over-expressed or under-expressed) across tissues in cattle. All 29 tissues showed DE NuMP genes in varying proportions of over-expression and under-expression. On the other hand, DE of MtMP genes was observed in < 50% of tissues and notably MtMP genes within a tissue was either all over-expressed or all under-expressed. A high proportion of NuMP (up to 60%) and MtMP (up to 100%) genes were over-expressed in tissues with expected high metabolic demand; heart, skeletal muscles and tongue, and under-expressed (up to 45% of NuMP, 77% of MtMP genes) in tissues with expected low metabolic rates; leukocytes, thymus, and lymph nodes. These tissues also invariably had the expression of all MtMP genes in the direction of dominant NuMP genes expression. The NuMP and MtMP genes were highly co-expressed across tissues and co-expression of genes in a cluster were non-random and functionally enriched for energy generation pathway. The differential gene expression and co-expression patterns were validated in independent cow and sheep datasets. CONCLUSIONS: The results of this study support the concept that there are biological interaction of MP genes from the mitochondrial and nuclear genomes given their over-expression in tissues with high energy demand and co-expression in tissues. This highlights the importance of considering MP genes from both genomes in future studies related to mitochondrial functions and traits related to energy metabolism.

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues.

BACKGROUND: Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and model species, we used sequence variants to map a type of expression quantitative trait loci (expression QTLs) that are associated with variations in the RNA splicing, i.e., sQTLs. To further the understanding of regulatory variants, sQTLs were compare with other two types of expression QTLs, 1) variants associated with variations in gene expression, i.e., geQTLs and 2) variants associated with variations in exon expression, i.e., eeQTLs, in different tissues. RESULTS: Using whole genome and RNA sequence data from four tissues of over 200 cattle, sQTLs identified using exon inclusion ratios were verified by matching their effects on adjacent intron excision ratios. sQTLs contained the highest percentage of variants that are within the intronic region of genes and contained the lowest percentage of variants that are within intergenic regions, compared to eeQTLs and geQTLs. Many geQTLs and sQTLs are also detected as eeQTLs. Many expression QTLs, including sQTLs, were significant in all four tissues and had a similar effect in each tissue. To verify such expression QTL sharing between tissues, variants surrounding (±1 Mb) the exon or gene were used to build local genomic relationship matrices (LGRM) and estimated genetic correlations between tissues. For many exons, the splicing and expression level was determined by the same cis additive genetic variance in different tissues. Thus, an effective but simple-to-implement meta-analysis combining information from three tissues is introduced to increase power to detect and validate sQTLs. sQTLs and eeQTLs together were more enriched for variants associated with cattle complex traits, compared to geQTLs. Several putative causal mutations were identified, including an sQTL at Chr6:87392580 within the 5th exon of kappa casein (CSN3) associated with milk production traits. CONCLUSIONS: Using novel analytical approaches, we report the first identification of numerous bovine sQTLs which are extensively shared between multiple tissue types. The significant overlaps between bovine sQTLs and complex traits QTL highlight the contribution of regulatory mutations to phenotypic variations.