Hypothalamus

The Iso-Seq method for sequencing full-length transcripts was developed by PacBio during the same time period as the genome assembly. We therefore used this technique to improve characterization of transcript isoforms expressed in cattle tissues using a diverse set of tissues collected from L1 Dominette 0 1449 upon euthanasia. The data were collected using an early version of the Iso-Seq library protocol [26 ] as suggested by PacBio. Briefly, RNA was extracted from each tissue using Trizol reagent as directed (Thermo Fisher). Then 2 μg of RNA were selected for PolyA tails and converted into complementary DNA (cDNA) using the SMARTer PCR cDNA Synthesis Kit (Clontech). The cDNA was amplified in bulk with 12–14 rounds of PCR in 8 separate reactions, then pooled and size-selected into 1–2, 2–3, and 3–6 kb fractions using the BluePippin instrument (Sage Science). Each size fraction was separately re-amplified in 8 additional reactions of 11 PCR cycles. The products for each size fraction amplification were pooled and purified using AMPure PB beads (Pacific Biosciences) as directed, and converted to SMRTbell libraries using the Template Prep Kit v1.0 (PacBio) as directed. Iso-Seq was conducted for 22 tissues including abomasum, aorta, atrium, cerebral cortex, duodenum, hypothalamus, jejunum, liver, longissimus dorsi muscle, lung, lymph node, mammary gland, medulla oblongata, omasum, reticulum, rumen, subcutaneous fat, temporal cortex, thalamus, uterine myometrium, and ventricle from the reference cow, as well as the testis of her sire. The size fractions were sequenced in either 4 (for the smaller 2 fractions) or 5 (for the largest fraction) SMRTcells on the RS II instrument. Isoforms were identified using the Cupcake ToFU pipeline [27 ] without using a reference genome.
Short-read–based RNA-seq data derived from tissues of Dominette were available in the GenBank database because her tissues have been a freely distributed resource for the research community. To complement and extend these data and to ensure that the tissues used for Iso-Seq were also represented by RNA-seq data for quantitative analysis and confirmation of isoforms observed in Iso-Seq, we generated additional data, avoiding overlap with existing public data. Specifically, the TruSeq stranded mRNA LT kit (Illumina, Inc.) was used as directed to create RNA-seq libraries, which were sequenced to ≥30 million reads for each tissue sample. The Dominette tissues that were sequenced in this study include abomasum, anterior pituitary, aorta, atrium, bone marrow, cerebellum, duodenum, frontal cortex, hypothalamus, KPH fat (internal organ fat taken from the covering on the kidney capsule), lung, lymph node, mammary gland (lactating), medulla oblongata, nasal mucosa, omasum, reticulum, rumen, subcutaneous fat, temporal cortex, thalamus, uterine myometrium, and ventricle. RNA-seq libraries were also sequenced from the testis of her sire. All public datasets, and the newly sequenced RNA-seq and Iso-Seq datasets, were used to annotate the assembly, to improve the representation of low-abundance and tissue-specific transcripts, and to properly annotate potential tissue-specific isoforms of each gene.

Fresh PFC and HIP tissues (1 mm × 1 mm × 1 mm) were obtained and placed on ice immediately after the mice were euthanized. The tissue was fixed with glutaraldehyde for 4 h, then 1% osmium buffer for 2 h, and finally dehydrated with gradient alcohol precipitation. After immersion in acetone/epoxy resin (2:1), acetone/epoxy resin (1:1), and epoxy resin solution, the tissue was then embedded in epoxy resin. The hypothalamus sample was cut into slices approximately 50 nm thick and then soaked in uranium dioxane acetate for 45 min to prepare the sample for observation under electron microscopy. Neuronal ultrastructure images were collected by the H-7650 transmission electron microscope.

Male BTBR T+ Itpr3tf/J (Jackson Laboratory #002282) mice were used to investigate the effects of adeno-associated virus (AAV) mediated hypothalamic TrkB.FL overexpression. Five cohorts of male mice were used—a long-term (24 wks), NCD (11% fat, caloric density 3.4 kcal/g, Teklad) fed cohort (n = 16); a long-term (23 wks), HFD (60% fat, caloric density 5.21 kcal/g, Research Diets, Inc. #D12492) fed cohort (n = 11); a short-term (4 wks) NCD fed cohort (n = 10); a short-term (4 wks) HFD fed cohort (n = 10), and a short-term C57BL/6 NCD fed cohort (n = 10). Ages of the mice were 15–17 weeks old (long-term NCD), 4–5 weeks old (long-term HFD), 4 weeks old (short-term NCD), 8–16 weeks old (short-term HFD), and 7–9 weeks old (short-term C57BL/6 NCD). For the HFD cohorts, mice were fed HFD for five weeks prior to AAV injections and maintained on the HFD for the duration of the studies. Weekly food consumption and body weights were recorded. One mouse from the short-term NCD cohort and one mouse from the short-term HFD cohort died during the study and were excluded from subsequent analysis. Experimental timelines for the long-term NCD and long-term HFD groups can be seen in Fig 1A and Fig 3A, respectively. All mice had ad libitum access to food and water. All mice were group housed (3–5 mice) in standard laboratory environment cages and housed in temperature (22–23°C) and humidity (30–70%) controlled rooms under a 12:12 light:dark cycle. All animal experiments were approved by The Ohio State University Institutional Animal Care and Use Committee.

Mice were sacrificed at 24 wpi (long-term NCD), 23 wpi (long-term HFD), and 4 wpi (short-term BTBR and C57BL/6 NCD and HFD BTBR). Mice were anesthetized by isoflurane and decapitated. Brown adipose tissue (BAT), gonadal WAT (gWAT), inguinal WAT (iWAT), and retroperitoneal WAT (rWAT), and liver were collected and weighed from both long-term groups. Gastrocnemius and pancreas were also dissected and weighed from the long-term NCD group. Hypothalamus was dissected from all groups. Tissues were flash-frozen on dry ice and stored at -80° C until further analysis.