Structure-based discovery of conformationally selective inhibitors of the serotonin transporter.

The serotonin transporter (SERT) removes synaptic serotonin and is the target of anti-depressant drugs. SERT adopts three conformations: outward-open, occluded, and inward-open. All known inhibitors target the outward-open state except ibogaine, which has unusual anti-depressant and substance-withdrawal effects, and stabilizes the inward-open conformation. Unfortunately, ibogaine's promiscuity and cardiotoxicity limit the understanding of inward-open state ligands. We docked over 200 million small molecules against the inward-open state of the SERT. Thirty-six top-ranking compounds were synthesized, and thirteen inhibited; further structure-based optimization led to the selection of two potent (low nanomolar) inhibitors. These stabilized an outward-closed state of the SERT with little activity against common off-targets. A cryo-EM structure of one of these bound to the SERT confirmed the predicted geometry. In mouse behavioral assays, both compounds had anxiolytic- and anti-depressant-like activity, with potencies up to 200-fold better than fluoxetine (Prozac), and one substantially reversed morphine withdrawal effects.

Autoantibody mimicry of hormone action at the thyrotropin receptor.

Thyroid hormones are vital in metabolism, growth and development1. Thyroid hormone synthesis is controlled by thyrotropin (TSH), which acts at the thyrotropin receptor (TSHR)2. In patients with Graves' disease, autoantibodies that activate the TSHR pathologically increase thyroid hormone activity3. How autoantibodies mimic thyrotropin function remains unclear. Here we determined cryo-electron microscopy structures of active and inactive TSHR. In inactive TSHR, the extracellular domain lies close to the membrane bilayer. Thyrotropin selects an upright orientation of the extracellular domain owing to steric clashes between a conserved hormone glycan and the membrane bilayer. An activating autoantibody from a patient with Graves' disease selects a similar upright orientation of the extracellular domain. Reorientation of the extracellular domain transduces a conformational change in the seven-transmembrane-segment domain via a conserved hinge domain, a tethered peptide agonist and a phospholipid that binds within the seven-transmembrane-segment domain. Rotation of the TSHR extracellular domain relative to the membrane bilayer is sufficient for receptor activation, revealing a shared mechanism for other glycoprotein hormone receptors that may also extend to other G-protein-coupled receptors with large extracellular domains.

Structure, function and pharmacology of human itch GPCRs.

The MRGPRX family of receptors (MRGPRX1-4) is a family of mas-related G-protein-coupled receptors that have evolved relatively recently1. Of these, MRGPRX2 and MRGPRX4 are key physiological and pathological mediators of itch and related mast cell-mediated hypersensitivity reactions2-5. MRGPRX2 couples to both Gi and Gq in mast cells6. Here we describe agonist-stabilized structures of MRGPRX2 coupled to Gi1 and Gq in ternary complexes with the endogenous peptide cortistatin-14 and with a synthetic agonist probe, respectively, and the development of potent antagonist probes for MRGPRX2. We also describe a specific MRGPRX4 agonist and the structure of this agonist in a complex with MRGPRX4 and Gq. Together, these findings should accelerate the structure-guided discovery of therapeutic agents for pain, itch and mast cell-mediated hypersensitivity.

Ultra-large library docking for discovering new chemotypes.

Despite intense interest in expanding chemical space, libraries containing hundreds-of-millions to billions of diverse molecules have remained inaccessible. Here we investigate structure-based docking of 170 million make-on-demand compounds from 130 well-characterized reactions. The resulting library is diverse, representing over 10.7 million scaffolds that are otherwise unavailable. For each compound in the library, docking against AmpC ß-lactamase (AmpC) and the D4 dopamine receptor were simulated. From the top-ranking molecules, 44 and 549 compounds were synthesized and tested for interactions with AmpC and the D4 dopamine receptor, respectively. We found a phenolate inhibitor of AmpC, which revealed a group of inhibitors without known precedent. This molecule was optimized to 77 nM, which places it among the most potent non-covalent AmpC inhibitors known. Crystal structures of this and other AmpC inhibitors confirmed the docking predictions. Against the D4 dopamine receptor, hit rates fell almost monotonically with docking score, and a hit-rate versus score curve predicted that the library contained 453,000 ligands for the D4 dopamine receptor. Of 81 new chemotypes discovered, 30 showed submicromolar activity, including a 180-pM subtype-selective agonist of the D4 dopamine receptor.

Genome-wide profiling the epigenetic landscape of histone variant TH2B in murine oocytes and pre-implantation embryos.

The histone variant TH2B, enriched in oocytes, sperm, and early embryos, decreases as embryos differentiate into pre-gastrula stages. Despite its presence, the role of TH2B in epigenetic reprogramming during early embryonic development remains largely under-researched. Our study employed ultra-low-input ChIP-seq (ULI-ChIP) to analyze the genome-wide distribution of TH2B in MII oocytes and early embryos. We found that TH2B is enriched in the chromatin of oocytes and 2-cell stage embryos but becomes less prevalent after the 2-cell stage. Correlation analysis revealed that the TH2B chromatin patterns in sperm and preimplantation embryos are more similar to each other than to those in MII oocytes. Gene ontology (GO) analysis of TH2B-occupied loci linked them to various developmental processes, including oogenesis, fertilization, chromatin modification, and transcription regulation. The study also identified a strong association of TH2B with specific transposable elements (TEs), particularly long terminal repeats (LTRs), which are known to regulate preimplantation development. Additionally, early embryos showed H3K9me3 marks at TH2B-bound loci. TH2B exhibited strong correlations with H2A.Z and H3.3 in the 2-cell and 8-cell stages, a positive association with H3K27Ac and H3K4me3, and a negative correlation with H3K27me3. Allelic reprogramming analysis of TH2B in embryos from C57BL/6J and DBA/2J crosses revealed differential dynamics between maternal and paternal alleles, with a notable paternal bias at the promoter in 2-cell embryos. Thus, TH2B's enrichment in early embryonic stages and its association with key regulatory regions and histone modifications underscore its importance in ZGA and subsequent developmental processes.

Morbidity and mortality in patients with stage IV pancreatic adenocarcinoma and acute cholangitis: Outcomes and risk prognostication.

BACKGROUND: Acute cholangitis (AC) is a common complication of pancreatic ductal adenocarcinoma (PDAC). Herein, we evaluated outcomes after the first AC episode and predictors of mortality and AC recurrence in patients with stage IV PDAC. METHODS: We conducted a single-center, retrospective observational study using institutional databases. Clinical data and outcomes for patients with stage IV PDAC and at least one documented episode of AC, were assessed. Overall survival (OS) was estimated using the Kaplan-Meier method, and Cox regression model was employed to identify predictors of AC recurrence and mortality. RESULTS: One hundred and twenty-four patients with stage IV PDAC and AC identified between January 01, 2014 and October 31, 2020 were included. Median OS after first episode of AC was 4.1 months (95 % CI, 4.0-5.5), and 30-day, 6, and 12-month survival was 86.2 % (95 % CI, 80.3-92.5), 37 % (95 % CI, 29.3-46.6 %) and 18.9 % (95 % CI, 13.1-27.3 %), respectively. Primary tumor in pancreatic body/tail (HR 2.29, 95 % CI: 1.26 to 4.18, p = 0.011), concomitant metastases to liver and other sites (HR 1.96, 95 % CI: 1.16 to 3.31, p = 0.003) and grade 3 AC (HR 2.26, 95 % CI: 1.45 to 3.52, p < 0.001), predicted worse outcomes. Intensive care unit admission, sepsis, systemic therapy, treatment regimen, and time to intervention did not predict survival or risk of recurrence of AC. CONCLUSIONS: AC confers significant morbidity and mortality in advanced PDAC. Worse outcomes are associated with higher grade AC, primary tumor location in pancreatic body/tail, and metastases to liver and other sites.

Energy penalties enhance flexible receptor docking in a model cavity.

Protein flexibility remains a major challenge in library docking because of difficulties in sampling conformational ensembles with accurate probabilities. Here, we use the model cavity site of T4 lysozyme L99A to test flexible receptor docking with energy penalties from molecular dynamics (MD) simulations. Crystallography with larger and smaller ligands indicates that this cavity can adopt three major conformations: open, intermediate, and closed. Since smaller ligands typically bind better to the cavity site, we anticipate an energy penalty for the cavity opening. To estimate its magnitude, we calculate conformational preferences from MD simulations. We find that including a penalty term is essential for retrospective ligand enrichment; otherwise, high-energy states dominate the docking. We then prospectively docked a library of over 900,000 compounds for new molecules binding to each conformational state. Absent a penalty term, the open conformation dominated the docking results; inclusion of this term led to a balanced sampling of ligands against each state. High ranked molecules were experimentally tested by Tm upshift and X-ray crystallography. From 33 selected molecules, we identified 18 ligands and determined 13 crystal structures. Most interesting were those bound to the open cavity, where the buried site opens to bulk solvent. Here, highly unusual ligands for this cavity had been predicted, including large ligands with polar tails; these were confirmed both by binding and by crystallography. In docking, incorporating protein flexibility with thermodynamic weightings may thus access new ligand chemotypes. The MD approach to accessing and, crucially, weighting such alternative states may find general applicability.

Pulmonary rehabilitation: A novel adjunct in management of obstructive sleep apnea.

Pulmonary rehabilitation (PR) is being used in the routine management of patients of obstructive sleep apnea (OSA) at some centers. However, the studies documenting benefits of PR in OSA lack standardization in terms of outcome measures. A study was hence planned to determine the efficacy of PR on exercise capacity, health related quality of life (HRQOL), day time sleepiness and sleep-quality of life (QOL) in patients of OSA. As a part of comprehensive therapy, patients diagnosed with OSA are managed with continuous positive airway pressure (CPAP), 8 weeks thrice weekly outpatient hospital-based PR and medical treatment at the Pulmonary Medicine Department, Government Medical College and Hospital, Chandigarh. However, some patients refuse for PR because of time constraints and travel issues. Patients with newly diagnosed OSA without co-existing respiratory disease, who agreed for the CPAP, PR and medical management were enrolled in group A. The patients who refused for PR but were ready for CPAP and medical management were enrolled in Group B; 30 patients were taken in each group. Exercise capacity, HRQOL, day time sleepiness and sleep-QOL were determined at baseline and at 8-weeks follow-up by 6-minute walk distance (6MWD), St. George's Respiratory Questionnaire (SGRQ), Epworth Sleepiness Scale (ESS) and Functional Outcomes of Sleep Questionnaire (FOSQ) and compared amongst the two groups. Four patients from group A were excluded as they did not complete PR; 26 patients from group A and 30 patients from group B were finally analyzed. At baseline, both groups were matched with respect to age, gender, apnea-hypopnea index (AHI), body mass index (BMI), FEV1%predicted, 6MWD, SGRQ, ESS and FOSQ. At follow up at 8 weeks, BMI, 6MWD, SGRQ, ESS and FOSQ improved significantly from baseline in group A (p<0.001). FEV1%predicted also improved but non significantly. In group B, FEV1%predicted, BMI, 6MWD, SGRQ, ESS and FOSQ score did not improve significantly from baseline. Mean improvement from baseline in BMI, 6MWD, SGRQ, ESS and FOSQ was significantly more in group A than group B (p<0.001, p<0.001, p=0.041, p<0.001 and p<0.001, respectively). PR, being beneficial, should be incorporated in standard management of OSA.

Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide.

The next challenge in synthetic biology is to be able to replicate synthetic nucleic acid sequences efficiently. The synthetic pair, 2-amino-8-(1-beta-d-2'- deoxyribofuranosyl) imidazo [1,2-a]-1,3,5-triazin-[8H]-4-one (trivially designated P) with 6-amino-3-(2'-deoxyribofuranosyl)-5-nitro-1H-pyridin-2-one (trivially designated Z), is replicated by certain Family A polymerases, albeit with lower efficiency. Through directed evolution, we identified a variant KlenTaq polymerase (M444V, P527A, D551E, E832V) that incorporates dZTP opposite P more efficiently than the wild-type enzyme. Here, we report two crystal structures of this variant KlenTaq, a post-incorporation complex that includes a template-primer with P:Z trapped in the active site (binary complex) and a pre-incorporation complex with dZTP paired to template P in the active site (ternary complex). In forming the ternary complex, the fingers domain exhibits a larger closure angle than in natural complexes but engages the template-primer and incoming dNTP through similar interactions. In the binary complex, although many of the interactions found in the natural complexes are retained, there is increased relative motion of the thumb domain. Collectively, our analyses suggest that it is the post-incorporation complex for unnatural substrates that presents a challenge to the natural enzyme and that more efficient replication of P:Z pairs requires a more flexible polymerase.

"Skinny" and "Fat" DNA: Two New Double Helices.

According to the iconic model, the Watson-Crick double helix exploits nucleobase pairs that are both size complementary (big purines pair with small pyrimidines) and hydrogen bond complementary (hydrogen bond donors pair with hydrogen bond acceptors). Using a synthetic biology strategy, we report here the discovery of two new DNA-like systems that appear to support molecular recognition with the same proficiency as standard Watson-Crick DNA. However, these both violate size complementarity (big pairs with small), retaining hydrogen bond complementarity (donors pair with acceptors) as their only specificity principle. They exclude mismatches as well as standard Watson-Crick DNA excludes mismatches. In crystal structures, these "skinny" and "fat" systems form the expected hydrogen bonds, while conferring novel minor groove properties to the resultant duplex regions of the DNA oligonucleotides. Further, computational tools, previously tested primarily on natural DNA, appear to work well for these two new molecular recognition systems, offering a validation of the power of modern computational biology. These new molecular recognition systems may have application in materials science and synthetic biology, and in developing our understanding of alternative ways that genetic information might be stored and transmitted.

Crystal structures of GCN2 protein kinase C-terminal domains suggest regulatory differences in yeast and mammals.

In response to amino acid starvation, GCN2 phosphorylation of eIF2 leads to repression of general translation and initiation of gene reprogramming that facilitates adaptation to nutrient stress. GCN2 is a multidomain protein with key regulatory domains that directly monitor uncharged tRNAs which accumulate during nutrient limitation, leading to activation of this eIF2 kinase and translational control. A critical feature of regulation of this stress response kinase is its C-terminal domain (CTD). Here, we present high resolution crystal structures of murine and yeast CTDs, which guide a functional analysis of the mammalian GCN2. Despite low sequence identity, both yeast and mammalian CTDs share a core subunit structure and an unusual interdigitated dimeric form, albeit with significant differences. Disruption of the dimeric form of murine CTD led to loss of translational control by GCN2, suggesting that dimerization is critical for function as is true for yeast GCN2. However, although both CTDs bind single- and double-stranded RNA, murine GCN2 does not appear to stably associate with the ribosome, whereas yeast GCN2 does. This finding suggests that there are key regulatory differences between yeast and mammalian CTDs, which is consistent with structural differences.

Structural basis for a six nucleotide genetic alphabet.

Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard "edge on" Watson-Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form. Another contained six consecutive Z:P pairs; it crystallized without a host in an A-form. In both structures, Z:P pairs fit canonical nucleobase hydrogen-bonding parameters and known DNA helical forms. Unique features include stacking of the nitro group on Z with the adjacent nucleobase ring in the A-form duplex. In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs, perhaps to accommodate the large nitro group on Z. Otherwise, ZP-rich DNA had many of the same properties as CG-rich DNA, a conclusion supported by circular dichroism studies in solution. The ability of standard duplexes to accommodate multiple and consecutive Z:P pairs is consistent with the ability of natural polymerases to biosynthesize those pairs. This, in turn, implies that the GACTZP synthetic genetic system can explore the entire expanded sequence space that additional nucleotides create, a major step forward in this area of synthetic biology.

The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition.

The spore photoproduct lesion (SP; 5-thymine-5,6-dihydrothymine) is the dominant photoproduct found in UV-irradiated spores of some bacteria such as Bacillus subtilis. Upon spore germination, this lesion is repaired in a light-independent manner by a specific repair enzyme: the spore photoproduct lyase (SP lyase). In this work, a host-guest approach in which the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) serves as the host and DNA as the guest was used to determine the crystal structures of complexes including 16 bp oligonucleotides with and without the SP lesion at 2.14 and 1.72 Šresolution, respectively. In contrast to other types of thymine-thymine lesions, the SP lesion retains normal Watson-Crick hydrogen bonding to the adenine bases of the complementary strand, with shorter hydrogen bonds than found in the structure of the undamaged DNA. However, the lesion induces structural changes in the local conformation of what is otherwise B-form DNA. The region surrounding the lesion differs significantly in helical form from B-DNA, and the minor groove is widened by almost 3 Šcompared with that of the undamaged DNA. Thus, these unusual structural features associated with SP lesions may provide a basis for recognition by the SP lyase.

Next generation of multispecific antibody engineering.

Multispecific antibodies recognize two or more epitopes located on the same or distinct targets. This added capability through protein design allows these man-made molecules to address unmet medical needs that are no longer possible with single targeting such as with monoclonal antibodies or cytokines alone. However, the approach to the development of these multispecific molecules has been met with numerous road bumps, which suggests that a new workflow for multispecific molecules is required. The investigation of the molecular basis that mediates the successful assembly of the building blocks into non-native quaternary structures will lead to the writing of a playbook for multispecifics. This is a must do if we are to design workflows that we can control and in turn predict success. Here, we reflect on the current state-of-the-art of therapeutic biologics and look at the building blocks, in terms of proteins, and tools that can be used to build the foundations of such a next-generation workflow.

Changes in Soft Tissue Variable of Lips Following Retraction of Anterioir Teeth- A Cephalometric Study.

Aim: The purpose of this study was to assess the short-term perioral soft tissue variations of the lips before and after treatment cases in 15 patients with bi-maxillary protrusion using treated lateral cephalograms who had already achieved active growth. Methodology: Fifteen pre-treatment and post-treatment lateral cephalometric radiographs of 18-25-year-old individuals with bimaxillary protrusion treated with all four 1st premolar extractions were accessed from the records. From the reference planes and landmarks, 13 horizontal, 10 vertical, and 2 angular measurements were noted. Statistical comparisons between pre-treatment and post-treatment measurements were measured by a paired t-test to assess the importance of the mean variations at the predetermined significance level. Pearson's correlation coefficient (R) was utilized to assess the strength and significance of the linear relationship between the mean differences for paired (dependent and independent) variables. Results: Pearson's correlation exhibited a noteworthy positive association between the horizontal changes in upper lip position and the horizontal changes of the upper incisor tip point (H-tU1) (R = 0.748), the upper incisor cervical point (H-cU1) (R = 0.707), the lower incisor tip point (H-tL1) (R = 0.839), and the lower incisor cervical point (H-cL1) (R = 0.767). This indicated that upper lip changes are the aftermath of the retraction of the upper and lower incisors in class I bi-maxillary protrusion malocclusion. Conclusion: Thick upper lips showed more retraction of the upper lip in correlation with retraction of the incisors as compared with thin lips. The lower incisor cervical point displayed the strongest association with lower lip retraction.

Effect of remineralizing agent on laser and nonlaser bleached enamel surfaces subjected to erosion: An in vitro study.

Aim: Assessment of remineralizing agent's effect on laser and nonlaser bleached enamel surfaces subjected to erosion. Materials and Methods: In this study, 80 extracted human permanent anteriors were collected and divided into 4 groups with 20 teeth per sample. Enamel specimen of 3 mm × 3 mm were made using polyvinyl chloride rings and acrylic and randomly divided into four groups. Then the specimens were subjected to initial microhardness test using Vicker's hardness tester (AVK-CO, Mitutoyo, Japan). Two indentations were placed at 100 mm from one another in the center of all the samples. Bleaching with laser and without laser using hydrogen peroxide was performed followed by remineralization in the groups (Groups 1a and 2a) and then were subjected to erosion. The final hardness was measured using the above method used for initial microhardness. Results: Microhardness in the remineralized groups showed least variation. The group in which laser bleaching was performed along with remineralization as compared with nonlaser bleaching group with remineralization showed improvement in microhardness but the data was not statistically significant. A significant difference was noted between the laser and remineralization group when compared with the groups in which no remineralization was done. Conclusion: After bleaching the enamel surface is more prone to erosion, so to improve the microhardness of bleached enamel a remineralizing agent should be used. A combination of diode laser bleaching and remineralizing agents leads to improved microhardness of the bleached enamel thus proving this combination to be efficacious.

Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase.

An under-explored target for SARS-CoV-2 is the S-adenosyl methionine (SAM)-dependent methyltransferase Nsp14, which methylates the N7-guanosine of viral RNA at the 5'-end, allowing the virus to evade host immune response. We sought new Nsp14 inhibitors with three large library docking strategies. First, up to 1.1 billion lead-like molecules were docked against the enzyme's SAM site, leading to three inhibitors with IC50 values from 6 to 50 µM. Second, docking a library of 16 million fragments revealed 9 new inhibitors with IC50 values from 12 to 341 µM. Third, docking a library of 25 million electrophiles to covalently modify Cys387 revealed 7 inhibitors with IC50 values from 3.5 to 39 µM. Overall, 32 inhibitors encompassing 11 chemotypes had IC50 values < 50 µM and 5 inhibitors in 4 chemotypes had IC50 values < 10 µM. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing starting points for future optimization.

Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.

Antiviral therapeutics to treat SARS-CoV-2 are needed to diminish the morbidity of the ongoing COVID-19 pandemic. A well-precedented drug target is the main viral protease (MPro ), which is targeted by an approved drug and by several investigational drugs. Emerging viral resistance has made new inhibitor chemotypes more pressing. Adopting a structure-based approach, we docked 1.2 billion non-covalent lead-like molecules and a new library of 6.5 million electrophiles against the enzyme structure. From these, 29 non-covalent and 11 covalent inhibitors were identified in 37 series, the most potent having an IC50 of 29 and 20 µM, respectively. Several series were optimized, resulting in low micromolar inhibitors. Subsequent crystallography confirmed the docking predicted binding modes and may template further optimization. While the new chemotypes may aid further optimization of MPro inhibitors for SARS-CoV-2, the modest success rate also reveals weaknesses in our approach for challenging targets like MPro versus other targets where it has been more successful, and versus other structure-based techniques against MPro itself.

Spectroscopic, electronic structure, molecular docking, and molecular dynamics simulation study of 7-Trifluoromethyl-1H-indole-2-carboxylic acid as an aromatase inhibitor.

The present work encompasses a combined experimental and theoretical investigation of the molecular structure, vibrational wavenumbers, electronic structure at the ground and electronic excited states, molecular electrostatic potential surface of 7-(Trifluoromethyl)-1H-indole-2-carboxylic acid (TICA) and possibility of the title molecule as an aromatase inhibitor using molecular docking and molecular dynamic simulations. A stable conformer has been obtained using potential energy scans by varying appropriate dihedral angles. The obtained minimum energy conformer was further optimized at the 6-311++G (d, p) basis set by applying the most accepted B3LYP functional. A good agreement between experimental and calculated normal modes of vibration has been observed. The hydrogen-bonded interaction between two monomeric units of TICA has been investigated using NBO,QTAIM, and NCI (noncovalent interactions) analysis. Molecular docking of TICA with human placental aromatase (PDB ID: 3S79) reveals the formation of polar hydrogen bonds as well as hydrophobic interactions between the ligand and the protein, right in the binding cavity. TICA satisfies all pharmacokinetic filters (Lipinski rule of five, the Veber rule, Ghose rule, Egan rule, as well as the Muegge rule) and has a high bioavailability score of 0.85. Dynamic stability of the ligand within the binding pocket of the target protein has been confirmed by 100 ns molecular dynamics simulation results. The present study provides an excellent starting point for additional in vivo research, and TICA may eventually serve as a significant therapeutic candidate for the treatment of breast cancer.

Heterogeneity in the Epigenetic Landscape of Murine Testis-Specific Histone Variants TH2A and TH2B Sharing the Same Bi-Directional Promoter.

Testis-specific histone variants are crucial to promote open chromatin structure to enable nucleosome disassembly in the final stages of spermiogenesis. However, even after histone replacement, mature sperm retain a proportion of these variants, the function of which is unknown. The present study aimed to understand the functional relevance of the retained H2B and H2A variants, TH2B and TH2A. While no literature is available on the phenotype of TH2A knockouts, TH2B/TH2A double knockout male mice are reported to be infertile. In this study, ChIP-seq analysis was done for TH2B and TH2A to understand the epigenomics of the retained TH2B and TH2A, using murine caudal sperm. Distribution across genomic partitions revealed ∼35% of the TH2B peaks within ±5 kb of TSS whereas TH2A peaks distribution was sparse at TSS. Gene Ontology revealed embryo development as the most significant term associated with TH2B. Also, based on genomic regions, TH2B was observed to be associated with spindle assembly and various meiosis-specific genes, which is an important finding as TH2A/TH2B DKO mice have been reported to have defective cohesin release. A comparison of mouse and human TH2B-linked chromatin revealed 26% overlap between murine and human TH2B-associated genes. This overlap included genes crucial for embryogenesis. Most importantly, heterogeneity in the epigenetic landscape of TH2A and TH2B was seen, which is intriguing as TH2B and TH2A are well reported to be present in the same nucleosomes to promote open chromatin. Additionally, unlike TH2B, TH2A was enriched on the mitochondrial chromosome. TH2A was found to be associated with Nuclear insertion of Mitochondrial DNA sequences (NUMTs) in sperm. A comprehensive analysis of these observations indicates novel functions for the sperm-retained TH2B and TH2A.