Filament Length Regulation Research Articles

Recessive TMOD1 mutation causes childhood cardiomyopathy

Familial cardiomyopathy in pediatric stages is a poorly understood presentation of heart disease in children that is attributed to pathogenic mutations. Through exome sequencing, we report a homozygous variant in tropomodulin 1 (TMOD1; c.565C>T, p.R189W) in three individuals from two unrelated families with childhood-onset dilated and restrictive cardiomyopathy. To decipher the mechanism of pathogenicity of the R189W mutation in TMOD1, we utilized a wide array of methods, including protein analyses, biochemistry and cultured cardiomyocytes. Structural modeling revealed potential defects in the local folding of TMOD1R189W and its affinity for actin. Cardiomyocytes expressing GFP-TMOD1R189W demonstrated longer thin filaments than GFP-TMOD1wt-expressing cells, resulting in compromised filament length regulation. Furthermore, TMOD1R189W showed weakened activity in capping actin filament pointed ends, providing direct evidence for the variant’s effect on actin filament length regulation. Our data indicate that the p.R189W variant in TMOD1 has altered biochemical properties and reveals a unique mechanism for childhood-onset cardiomyopathy.

Emergence and maintenance of variable-length actin filaments in a limiting pool of building blocks

Actin is one of the key structural components of the eukaryotic cytoskeleton that regulates cellular architecture and mechanical properties. Dynamic regulation of actin filament length and organization is essential for the control of many physiological processes including cell adhesion, motility and division. While previous studies have mostly focused on the mechanisms controlling the length of single actin filaments, it remains poorly understood how distinct actin filament populations in cells maintain different lengths using the same set of molecular building blocks. Here, we develop a theoretical model for the length regulation of multiple actin filaments by nucleation and growth-rate modulation by actin-binding proteins in a limiting pool of monomers. We first show that spontaneous nucleation of actin filaments naturally leads to heterogeneities in filament length distribution. We then investigate the effects of filament growth inhibition by capping proteins and growth promotion by formin proteins on filament length distribution. We find that filament length heterogeneity can be increased by growth inhibition, whereas growth promoters do not significantly affect length heterogeneity. Interestingly, a competition between filament growth inhibitors and growth promoters can give rise to bimodal filament length distribution as well as a highly heterogeneous length distribution with large statistical dispersion. We quantitatively predict how heterogeneity in actin filament length can be modulated by tuning filamentous actin nucleation and growth rates in order to create distinct filament subpopulations with different lengths.

The Mechanisms of Thin Filament Assembly and Length Regulation in Muscles.

The actin containing tropomyosin and troponin decorated thin filaments form one of the crucial components of the contractile apparatus in muscles. The thin filaments are organized into densely packed lattices interdigitated with myosin-based thick filaments. The crossbridge interactions between these myofilaments drive muscle contraction, and the degree of myofilament overlap is a key factor of contractile force determination. As such, the optimal length of the thin filaments is critical for efficient activity, therefore, this parameter is precisely controlled according to the workload of a given muscle. Thin filament length is thought to be regulated by two major, but only partially understood mechanisms: it is set by (i) factors that mediate the assembly of filaments from monomers and catalyze their elongation, and (ii) by factors that specify their length and uniformity. Mutations affecting these factors can alter the length of thin filaments, and in human cases, many of them are linked to debilitating diseases such as nemaline myopathy and dilated cardiomyopathy.

Shortening the thick filament by partial deletion of titin's C-zone alters cardiac function by reducing the operating sarcomere length range

Titin's C-zone is an inextensible segment in titin, comprised of 11 super-repeats and located in the cMyBP-C-containing region of the thick filament. Previously we showed that deletion of titin's super-repeats C1 and C2 (TtnΔC1–2 model) results in shorter thick filaments and contractile dysfunction of the left ventricular (LV) chamber but that unexpectedly LV diastolic stiffness is normal. Here we studied the contraction-relaxation kinetics from the time-varying elastance of the LV and intact cardiomyocyte, cellular work loops of intact cardiomyocytes, Ca2+ transients, cross-bridge kinetics, and myofilament Ca2+ sensitivity. Intact cardiomyocytes of TtnΔC1–2 mice exhibit systolic dysfunction and impaired relaxation. The time-varying elastance at both LV and single-cell levels showed that activation kinetics are normal in TtnΔC1–2 mice, but that relaxation is slower. The slowed relaxation is, in part, attributable to an increased myofilament Ca2+ sensitivity and slower early Ca2+ reuptake. Cross-bridge dynamics showed that cross-bridge kinetics are normal but that the number of force-generating cross-bridges is reduced. In vivo sarcomere length (SL) measurements revealed that in TtnΔC1–2 mice the operating SL range of the LV is shifted towards shorter lengths. This normalizes the apparent cell and LV diastolic stiffness but further reduces systolic force as systole occurs further down on the ascending limb of the force-SL relation. We propose that the reduced working SLs reflect titin's role in regulating diastolic stiffness by altering the number of sarcomeres in series. Overall, our study reveals that thick filament length regulation by titin's C-zone is critical for normal cardiac function.

Abstract P315: Shortening The Thick Filament By Partial Deletion Of Titin’S C-zone Alters Cardiac Function By Reducing The Operating Sarcomere Length Range Of The Heart.

Titin’s C-zone is the inextensible part of titin that binds along the thick filament at its cMyBP-C -containing region. Previously it was shown that deletion of titin’s super-repeats C1 and C2 ( Ttn ΔC1-2 mouse model) results in shorter thick filaments and contractile dysfunction, but LV chamber stiffness is normal. Here we studied the contraction-relaxation kinetics from the time-varying elastance of the left ventricle (LV) and from cellular work loops of intact loaded cardiac myocytes. Ca 2+ transients were also measured as well as crossbridge cycling kinetics and Ca 2+ sensitivity of force. It was found that intact cardiomyocytes of Ttn ΔC1-2 mice exhibit systolic dysfunction and impaired relaxation. The time-varying elastance of the LV chamber showed that the kinetics of LV activation are normal but that relaxation is slower in Ttn ΔC1-2 mice. The slowed relaxation was, in part, attributable to an increased myofilament Ca 2+ sensitivity and slower early Ca 2+ reuptake. Dynamic stiffness at the myofilament level showed that cross-bridge kinetics are normal, but that the number of force-generating cross-bridges is reduced. In vivo sarcomere length (SL) measurements in the mid-wall region of the LV revealed that the operating SL range is shifted in Ttn ΔC1-2 mice towards shorter lengths. This normalizes the apparent cell and LV chamber stiffness but reduces the number of force generating cross-bridges due to suboptimal thin and thick filament overlap. Thus the contractile dysfunction in Ttn ΔC1-2 mice is not only due to shorter thick filaments but also to a reduced operating sarcomere length range. Overall these results reveal that for normal cardiac function, thick filament length regulation by titin’s C-zone is critical.

Leiomodin creates a leaky cap at the pointed end of actin-thin filaments.

Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a "swinging gate" allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.

Regulation of Actin Filament Length by Muscle Isoforms of Tropomyosin and Cofilin.

In striated muscle the extent of the overlap between actin and myosin filaments contributes to the development of force. In slow twitch muscle fibers actin filaments are longer than in fast twitch fibers, but the mechanism which determines this difference is not well understood. We hypothesized that tropomyosin isoforms Tpm1.1 and Tpm3.12, the actin regulatory proteins, which are specific respectively for fast and slow muscle fibers, differently stabilize actin filaments and regulate severing of the filaments by cofilin-2. Using in vitro assays, we showed that Tpm3.12 bound to F-actin with almost 2-fold higher apparent binding constant (Kapp) than Tpm1.1. Cofilin2 reduced Kapp of both tropomyosin isoforms. In the presence of Tpm1.1 and Tpm3.12 the filaments were longer than unregulated F-actin by 25% and 40%, respectively. None of the tropomyosins affected the affinity of cofilin-2 for F-actin, but according to the linear lattice model both isoforms increased cofilin-2 binding to an isolated site and reduced binding cooperativity. The filaments decorated with Tpm1.1 and Tpm3.12 were severed by cofilin-2 more often than unregulated filaments, but depolymerization of the severed filaments was inhibited. The stabilization of the filaments by Tpm3.12 was more efficient, which can be attributed to lower dynamics of Tpm3.12 binding to actin.

Directional allosteric regulation of protein filament length.

Cofilin and ADF are cytoskeleton remodeling proteins that cooperatively bind and fragment actin filaments. Bound cofilin molecules do not directly interact with each other, indicating that cooperative binding of cofilin is mediated by the actin filament lattice. Cofilactin is therefore a model system for studying allosteric regulation of self-assembly. How cofilin binding changes structural and mechanical properties of actin filaments is well established. Less is known about the interaction energies and the thermodynamics of filament fragmentation, which describes the collective manner in which the cofilin concentration controls mean actin filament length. Here, we provide a general thermodynamic framework for allosteric regulation of self-assembly, and we use the theory to predict the interaction energies of experimental actin filament length distributions over a broad range of cofilin binding densities and for multiple cofilactin variants. We find that bound cofilin induces changes in nearby actin-actin interactions, and that these allosteric effects are propagated along the filament to affect up to four neighboring cofilin-binding sites (i.e., beyond nearest-neighbor allostery). The model also predicts that cofilin differentially stabilizes and destabilizes longitudinal versus lateral actin-actin interactions, and that the magnitude, range, asymmetry, and even the sign of these interaction energies can be altered using different actin and cofilin mutational variants. These results demonstrate that the theoretical framework presented here can provide quantitative thermodynamic information governing cooperative protein binding and filament length regulation, thus revealing nanometer length-scale interactions from micron length-scale "wet-lab" measurements.

Design and Optimization of Tropomyosin Fragments for Tropomodulin Interaction Studies

Monomeric actin, or G-actin, polymerizes into filamentous actin, or F-actin which is an important component of cellular structures controlling many processes including vesicle trafficking, cell motility, inter and intracellular transport, and muscle contraction. Actin filaments are composed of a pointed end (slow growing) and a barbed end (fast growing). Interactions at each end enables control of the length of actin filaments. Tropomodulin (Tmod1-4) modulates actin filament length by interacting with tropomyosin (Tpm) and actin at the pointed end of the filament. Tmod binds two Tpm molecules through two distinct Tpm binding sites. Establishing the structure of each Tmod-Tpm binding interface is critical to understand the thin filament length regulation mechanism of Tmod. To facilitate NMR structure determination, we have established the optimal size of Tpm fragment necessary to form respective stable complexes. The four fragments we designed were residues 1-43, 1-33, 1-26 or 1-19 of Tpm1.8 fused with a GCN4 sequence promoting coiled-coil formation. We used NMR to determine and compare spectral effects between the optimized Tpm fragments and Tpm-binding sites of Tmod2. A significant change in spectra occurred when length of Tpm sequence changed from 19 to 26 residues and with almost no change with further increase in Tpm sequence length. Stability of the designed Tpm fragments and their affinity for Tpm-binding sites on Tmod2 were evaluated by CD spectroscopy. Our results revealed that Tpm1.8 fragments containing residues 1-19 and 1-43 were more stable with a melting temperature of 44 and 52oC, respectively, however, the 1-19 fragment was not long enough to represent the whole binding interface. The calculated dissociation constants showed strong affinity of Tmod2 for the Tpm1.8 1-43. Therefore, Tpm1.8-1-43 fragment is the most optimal for use in NMR studies to further study its interaction with Tmod.

Experimentally Varying the Number of Super-Repeats in the Neb Gene of the Mouse - Assessing the Role of Nebulin in Thin Filament Length Regulation

Nebulin is a giant, modular actin binding protein that spans along the thin filament in skeletal muscle. Nebulin consists of numerous tandem copies of 38.5 nm ‘super-repeats’ that correspond to the arrangement of troponin and tropomyosin on the thin filament. Besides being known as a thin filament stabilizer, nebulin has been speculated to act as a thin filament ruler in skeletal muscle, yet little is known about nebulin's direct influence on actin length or its mechanism of action. Here we developed two novel mouse models in which nebulin super-repeats 9-11 are deleted (NebΔSR9-11) or duplicated (NebdupSR9-11), respectively. Mice of either model are viable and develop without muscle weight deficits. Super-resolution microscopy (SR-SIM) and immunoelectron microscopy on extensor digitorum longus (EDL) muscle revealed that the N-terminus of nebulin, together with tropomodulin (Tmod) localizes at the thin filament pointed end. Furthermore, nebulin and thin filaments were found to be shorter by ∼115 nm in NebΔSR9-11 and longer by ∼115 nm in NebdupSR9-11 EDL. Compound heterozygous animals (NebΔSR9-11,dupSR9-11) express both the shorter and the longer nebulin close to a ratio of 1:1 and the difference in their lengths is ∼230 nm. Tmod localization suggests a bimodal thin filament length distribution in NebΔSR9-11,dupSR9-11 EDL muscle fibers according to the shorter and longer nebulin. Functional studies on skinned EDL fibers revealed leftward shift of the descending limb of the force-sarcomere length relationship in NebΔSR9-11 and rightward shift in NebdupSR9-11 consistent with their altered thin filament lengths. We conclude that nebulin rules the thin filaments in EDL muscle with each of nebulin's super-repeats being responsible for a quantal 38 nm thin filament length. Studies on other muscle types are currently ongoing.

Role of intrinsic disorder in muscle sarcomeres.

The role and utility of intrinsically disordered regions (IDRs) is reviewed for two groups of sarcomeric proteins, such as members of tropomodulin/leiomodin (Tmod/Lmod) protein homology group and myosin binding protein C (MyBP-C). These two types of sarcomeric proteins represent very different but strongly interdependent functions, being responsible for maintaining structure and operation of the muscle sarcomere. The role of IDRs in the formation of complexes between thin filaments and Tmods/Lmods is discussed within the framework of current understanding of the thin filament length regulation. For MyBP-C, the function of IDRs is discussed in the context of MYBP-C-dependent sarcomere contraction and actomyosin activation.

Nebulin Stiffens the Thin Filament and Augments Crossbridge Interaction - An X-Ray Diffraction Study on Intact Muscle

Nebulin, the giant sarcomeric protein is thought to play a role in thin filament length regulation but little is known about nebulin's influence on the thin filament structure in skeletal muscle. In the present work we compared the ultrastructure of relaxed and contracting intact soleus muscle dissected from conditional nebulin-knockout (cKO) and control (Ctrl) mice by using small-angle X-ray diffraction. Although the spacing of the actin subunit repeats (27.3 Å meridional reflection) was equal in both groups in relaxed muscles, during contraction the normalized percent change is more than the double in cKO (0.0054%/kPa) compared to that of the control (0.0020%/kPa). The myofibrillar area was determined by a detailed cross-sectional ultrastructural analysis thereby making the stiffness calculation of single thin filaments possible. The stiffness for 1-μm-long actin was calculated to be 38.7 pN/nm in Ctrl muscle and 14.8 pN/nm in cKO soleus. Furthermore, significantly shorter left-handed thin filament helical pitch (59 Å meridional reflection) was found in the absence of nebulin in passive muscles (58.88 Å in cKO vs. 59.14 Å in Ctrl); the shorter 59 Å helical pitch was maintained during contraction. Through the equatorial 1,0 and 1,1 intensities we found significantly less mass attached to the thin filaments in passive cKO muscles and inefficient myosin mass transfer during their contraction. According to our findings, nebulin plays a role in the passive state of muscle by fine-adjusting the 59 Å helical pitch of the thin filaments thereby modulating the binding sites of regulatory proteins along the long pitch groove of actin. Further, nebulin stiffens the thin filament which is critically important for skeletal muscle force development, explaining why the absence of the nebulin in nemaline myopathy patients leads to muscle weakness.

The Giant Protein Titin Regulates the Length of the Striated Muscle Thick Filament-Titin Rules

The contractile machinery of heart and skeletal muscles that powers life has as its most essential component the thick filament, comprised of the molecular motor myosin. The thick filament is of a precisely controlled length, defining thereby the force level that muscles generate and how this force varies with muscle length. It has been speculated that the mechanism by which the length of the thick filament is so exquisitely controlled involves the giant protein titin, but no conclusive support for or against exists. Here we show studies on a mouse model in which we deleted two of titin's C-zone super-repeats, located in the A-band region of the sarcomere. Structural studies using immunoelectron microscopy and super-resolution optical microscopy in both cardiac and skeletal muscles reveal a thick filament length that is reduced by ∼170 nm; functional studies reveal reduced force generation and a dilated cardiomyopathy (DCM) phenotype. Our studies show for the first time the important role of titin in regulating thick filament length, with each of titin's C-zone repeats being responsible for a quantal 43 nm thick filament length. We conclude that thick filament length regulation is titin-based and that this mechanism is crucial for maintaining muscle health.

The comparison of alternative splicing among the multiple tissues in cucumber

BackgroundAlternative splicing (AS) is an important post-transcriptional process. It has been suggested that most AS events are subject to tissue-specific regulation. However, the global dynamics of AS in different tissues are poorly explored.ResultsTo analyse global changes in AS in multiple tissues, we identified the AS events and constructed a comprehensive catalogue of AS events within each tissue based on the genome-wide RNA-seq reads from ten tissues in cucumber. First, we found that 58% of the multi-exon genes underwent AS. We further obtained 565 genes with significantly more AS events compared with random genes. These genes were found significant enrichment in biological processes related to the regulation of actin filament length. Second, significantly different AS event profiles among ten tissues were found. The tissues with the same origin of development are more likely to have a relatively similar AS profile. Moreover, 7370 genes showed tissue-specific AS events and were highly enriched in biological processes related to the positive regulation of cellular component organization. Root-specificity AS genes were related to the cellular response to DNA damage stimulus. Third, the genes with different intron retention (IR) patterns among the ten tissues showed significant difference in GC percentages of the retained intron, and the number of exons and FPKM of the major transcripts.ConclusionsOur study provided a comprehensive view of AS in multiple tissues. We revealed novel insights into the patterns of AS in multiple tissues and the tissue-specific AS in cucumber.

The giant protein titin regulates the length of the striated muscle thick filament

The contractile machinery of heart and skeletal muscles has as an essential component the thick filament, comprised of the molecular motor myosin. The thick filament is of a precisely controlled length, defining thereby the force level that muscles generate and how this force varies with muscle length. It has been speculated that the mechanism by which thick filament length is controlled involves the giant protein titin, but no conclusive support for this hypothesis exists. Here we show that in a mouse model in which we deleted two of titin’s C-zone super-repeats, thick filament length is reduced in cardiac and skeletal muscles. In addition, functional studies reveal reduced force generation and a dilated cardiomyopathy (DCM) phenotype. Thus, regulation of thick filament length depends on titin and is critical for maintaining muscle health.

Titin and Nebulin in Thick and Thin Filament Length Regulation.

In this review we discuss the history and the current state of ideas related to the mechanism of size regulation of the thick (myosin) and thin (actin) filaments in vertebrate striated muscles. Various hypotheses have been considered during of more than half century of research, recently mostly involving titin and nebulin acting as templates or 'molecular rulers', terminating exact assembly. These two giant, single-polypeptide, filamentous proteins are bound in situ along the thick and thin filaments, respectively, with an almost perfect match in the respective lengths and structural periodicities. However, evidence still questions the possibility that the proteins function as templates, or scaffolds, on which the thin and thick filaments could be assembled. In addition, the progress in muscle research during the last decades highlighted a number of other factors that could potentially be involved in the mechanism of length regulation: molecular chaperones that may guide folding and assembly of actin and myosin; capping proteins that can influence the rates of assembly-disassembly of the myofilaments; Ca2+ transients that can activate or deactivate protein interactions, etc. The entire mechanism of sarcomere assembly appears complex and highly dynamic. This mechanism is also capable of producing filaments of about the correct size without titin and nebulin. What then is the role of these proteins? Evidence points to titin and nebulin stabilizing structures of the respective filaments. This stabilizing effect, based on linear proteins of a fixed size, implies that titin and nebulin are indeed molecular rulers of the filaments. Although the proteins may not function as templates in the assembly of the filaments, they measure and stabilize exactly the same size of the functionally important for the muscles segments in each of the respective filaments.

Tropomodulin 1 directly controls thin filament length in both wild-type and tropomodulin 4-deficient skeletal muscle

The sarcomeric tropomodulin (Tmod) isoforms Tmod1 and Tmod4 cap thin filament pointed ends and functionally interact with the leiomodin (Lmod) isoforms Lmod2 and Lmod3 to control myofibril organization, thin filament lengths, and actomyosin crossbridge formation in skeletal muscle fibers. Here, we show that Tmod4 is more abundant than Tmod1 at both the transcript and protein level in a variety of muscle types, but the relative abundances of sarcomeric Tmods are muscle specific. We then generate Tmod4−/− mice, which exhibit normal thin filament lengths, myofibril organization, and skeletal muscle contractile function owing to compensatory upregulation of Tmod1, together with an Lmod isoform switch wherein Lmod3 is downregulated and Lmod2 is upregulated. However, RNAi depletion of Tmod1 from either wild-type or Tmod4−/− muscle fibers leads to thin filament elongation by ∼15%. Thus, Tmod1 per se, rather than total sarcomeric Tmod levels, controls thin filament lengths in mouse skeletal muscle, whereas Tmod4 appears to be dispensable for thin filament length regulation. These findings identify Tmod1 as the key direct regulator of thin filament length in skeletal muscle, in both adult muscle homeostasis and in developmentally compensated contexts.

Tropomodulin 1 directly controls thin filament length in both wild-type and tropomodulin 4-deficient skeletal muscle.

The sarcomeric tropomodulin (Tmod) isoforms Tmod1 and Tmod4 cap thin filament pointed ends and functionally interact with the leiomodin (Lmod) isoforms Lmod2 and Lmod3 to control myofibril organization, thin filament lengths, and actomyosin crossbridge formation in skeletal muscle fibers. Here, we show that Tmod4 is more abundant than Tmod1 at both the transcript and protein level in a variety of muscle types, but the relative abundances of sarcomeric Tmods are muscle specific. We then generate Tmod4(-/-) mice, which exhibit normal thin filament lengths, myofibril organization, and skeletal muscle contractile function owing to compensatory upregulation of Tmod1, together with an Lmod isoform switch wherein Lmod3 is downregulated and Lmod2 is upregulated. However, RNAi depletion of Tmod1 from either wild-type or Tmod4(-/-) muscle fibers leads to thin filament elongation by ∼15%. Thus, Tmod1 per se, rather than total sarcomeric Tmod levels, controls thin filament lengths in mouse skeletal muscle, whereas Tmod4 appears to be dispensable for thin filament length regulation. These findings identify Tmod1 as the key direct regulator of thin filament length in skeletal muscle, in both adult muscle homeostasis and in developmentally compensated contexts.

The switch role of the Tmod4 in the regulation of balanced development between myogenesis and adipogenesis

Tmod4 (Tropomodulin 4) is a member of Tmod family that plays important role in thin filament length regulation and myofibril assembly. We found that the expression levels of Tmod4 were higher in skeletal muscle and adipose tissues. However, the function and regulation of the Tmod4 gene in the myogenesis and adipogenesis remains unclear. In this study, we found that the expression of Tmod4 was decreased in myogenesis while increased in adipogenesis. Then, the transcriptional regulation analysis of Tmod4 promoter showed that Tmod4 could be regulated directly by myogenic factors and adipogenic factors. Furthermore, the roles of Tmod4 in the myogenesis and adipogenesis were confirmed by its over-expression in C2C12 cells and 3T3 cells, which suggested that Tmod4 could promote adipogenesis by up-regulating the adipogenic factors but moderately delay the myogenesis. These results indicated that the Tmod4 gene may play as a switch between myogenesis and adipogenesis, which resulted in the balanced development between skeletal muscle and adipose tissue. Therefore, the model for switch role of the Tmod4 in the balanced regulation between myogenesis and adipogenesis was proposed. It is showed that the expression of Tmod4 was activated in adipogenesis by adipogenic factors while inhibited in myogenesis by myogenic factors. Moreover, Tmod4 could promote adipogenesis by up-regulating the expression of adipogenic factors while moderately delaying the myogenesis. Our study provides an important basis for further understanding the regulation and function of porcine Tmod4 in muscle and fat development.

Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity

BackgroundHanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s without the introduction of foreign germplasm. Since 1979, Hanwoo has been bred as beef cattle. Genetic variation was analyzed by whole-genome deep resequencing of a Hanwoo bull. The Hanwoo genome was compared to that of two other breeds, Black Angus and Holstein, and genes within regions of homozygosity were investigated to elucidate the genetic and genomic characteristics of Hanwoo.ResultsThe Hanwoo bull genome was sequenced to 45.6-fold coverage using the ABI SOLiD system. In total, 4.7 million single-nucleotide polymorphisms and 0.4 million small indels were identified by comparison with the Btau4.0 reference assembly. Of the total number of SNPs and indels, 58% and 87%, respectively, were novel. The overall genotype concordance between the SNPs and BovineSNP50 BeadChip data was 96.4%. Of 1.6 million genetic differences in Hanwoo, approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Among 1,045 genes containing reliable specific NS/SS/Is in Hanwoo, 109 genes contained more than one novel damaging NS/SS/I. Of the genes containing NS/SS/Is, 610 genes were assigned as trait-associated genes. Moreover, 16, 78, and 51 regions of homozygosity (ROHs) were detected in Hanwoo, Black Angus, and Holstein, respectively. ‘Regulation of actin filament length’ was revealed as a significant gene ontology term and 25 trait-associated genes for meat quality and disease resistance were found in 753 genes that resided in the ROHs of Hanwoo. In Hanwoo, 43 genes were located in common ROHs between whole-genome resequencing and SNP chips in BTA2, 10, and 13 coincided with quantitative trait loci for meat fat traits. In addition, the common ROHs in BTA2 and 16 were in agreement between Hanwoo and Black Angus.ConclusionsWe identified 4.7 million SNPs and 0.4 million small indels by whole-genome resequencing of a Hanwoo bull. Approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Additionally, we found 25 trait-associated genes for meat quality and disease resistance among 753 genes that resided in the ROHs of Hanwoo. These findings will provide useful genomic information for identifying genes or casual mutations associated with economically important traits in cattle.