Evidence of linkage between high-glycine-tyrosine keratin gene loci and wool fibre diameter in a Merino half-sib family

Candidate genes for quantitative trait loci have been studied in a Medium Peppin Merino flock. Obvious candidates for effects on wool production traits are genes for the major proteins expressed in the wool fibre, the keratin and keratin-associated protein genes. Two keratin-associated protein loci, KRTAP6 and KRTAP8, have previously been shown to be linked. The results of analyses between these two loci and production traits gave significant evidence of linkage with wool fibre diameter in one out of eight halfsib groups tested. High-glycine-tyrosine proteins (KRTAP6, 7 and 8) are known to vary considerably in abundance in wool fibres and it is possible that a gene for major effect on fibre diameter is located within the same chromosomal region as KRTAP6 and KRTAP8.     

Search for variation in the ovine KAP7-1 and KAP8-1 genes using polymerase chain reaction-single-stranded conformational polymorphism screening

Keratins and keratin-associated proteins (KAPs) are large heterogeneous groups of proteins that constitute about 90% of the wool fiber. The genes encoding the high glycine-tyrosine (HGT) KAPs are the first sub-group of KAP genes expressed in the wool follicle and just after expression of the keratin genes. Little is known about variation in these genes, which led us to investigate two HGT-KAP genes, KRTAP7-1 and KRTAP8-1. Polymerase chain reaction-single-stranded conformational polymorphism analysis was used to investigate these genes in 250 Romney-cross sheep. For KRTAP7-1, two unique banding patterns were detected for amplicons that spanned the entire coding region. Sequencing confirmed the presence of two sequences with only one nucleotide difference (c.173G/A) putatively resulting in p.Ser58Asn. One was identical to the published ovine KRTAP7-1 sequence. For KRTAP8-1, five unique banding patterns were detected in an amplicon that spanned the entire coding region. Sequencing revealed five different DNA sequences, all of which were highly homologous to the previously reported ovine KRTAP8-1 sequence. Among these five sequences, four single-nucleotide substitutions were identified and three of them were located in the coding region. One of these was nonsynonymous and would putatively result in p.Tyr34Asn. The variation detected in KRTAP7-1 and KRTAP8-1 may influence their expression or protein structure.     

Cashmere production,skin characteristics,and mutated genes in crimped cashmere fibre goats

A subpopulation of Yanshan cashmere goats with crimped fibre has emerged in a closed population in recent years, but little is known about differences in cashmere production performance, skin characteristics, and fibre-style-related genes between goats with different cashmere fibre styles. Therefore, the aim of this study was to investigate fibre characteristics, cashmere yield, hair follicle traits, and fibre-style-related genes in cashmere goats with the two cashmere fleece styles—non-crimped and crimped. Based on the cashmere fibre type, 80 six-month-old female Yanshan cashmere goats were used in this study: 40 goats with non-crimped fleece (NCF) and 40 with crimped fleece (CF). The growth performance and cashmere production of the goats were recorded. Skin samples were collected to determine hair follicle traits and gene sequencing. The results indicated that there were no differences in initial live weight, final live weight, average daily feed intake, and average daily gain between the two groups of goats (P > 0.05). The total yield of cashmere and the stretched length of fibre of the CF goats were higher (P < 0.01 and P < 0.05, respectively) and fibre diameter was lower (P < 0.05) than that of the NCF goats. There were no between-group differences in the density and activity of primary and secondary hair follicles, secondary-to-primary fibre ratio, depth of primary follicles, or epidermal thickness. However, the depth of secondary follicles and dermal thickness were higher (P < 0.05) in NCF goats than in CF goats. There were mutations in the KRT5, KAP8, KRT8, KRT74, KRT34, KRT1, KRT71, KRT6A, KAP6, KRT81, and KRT83 genes, four of which caused amino acid changes. The allele and genotype frequencies of base mutations in the KRT5, KAP8, KRT34, KRT1, KRT6A, KRT81, and KRT83 genes were different in the NCF and CF goats (P < 0.05). The distribution and content of the secondary structure elements and tertiary structures of proteins differed between the wide-type and mutated KRT1 and KRT6A proteins. KRT1, KRT6A, KRT71, and TGFα mRNA expression levels were significantly higher in CF goats than in NCF goats (P < 0.05). It is concluded that cashmere goats that have fleece with crimped fibres produce a greater yield of fleece with finer diameter fibres than those with conventional straight cashmere fibres. These differences in fibre properties may be associated with mutations in the genes coding for KRT1 and KRT6A.     

Identification of microRNAs in Wool Follicles during Anagen,Catagen, and Telogen Phases in Tibetan Sheep

Background

Wool quality is one of the most important economic traits in sheep. The wool fiber is derived from specialized skin cells that are referred to as wool follicles. To understand the roles of microRNAs (miRNAs) in wool fiber growth, we detected the expression patterns of miRNAs in wool follicles at the anagen, catagen, and telogen stages from Tibetan sheep through Solexa sequencing.

Results

A total of 244 mature miRNAs were identified. Of these, only five miRNAs are listed in the database of sheep miRNAs (miRBase Database V19), and the other 239 miRNAs have not been previously described in this species. Further analyses indicated that 204 miRNAs are evolutionarily conserved among mammal species, whereas 35 of the identified miRNAs were first found specifically in sheep. The expression pattern analyses showed that the expression levels of 39, 34, and 20 of the miRNAs significantly change between anagen and catagen, between anagen and telogen, and between catagen and telogen, respectively. The results of the bioinformatics analysis show that these differentially expressed miRNAs might regulate wool follicle development by targeting genes in many different pathways, such as the MAPK and Wnt pathways, as well as the pathways that regulate the actin cytoskeleton, focal adhesion, and tight junctions. Furthermore, we identified six differentially expressed miRNAs (oar-miR-103-3P, oar-miR-148b-3P, oar-miR-320-3P, oar-miR-31-5P, oar-novel-1-5P, and oar-novel-2-3P) that might target the key genes of the Wnt pathway. It has been reported that the Wnt pathway is critical for wool follicle development. Therefore, these miRNAs may regulate wool development through the Wnt pathway.

Conclusions

Our results provide new information on the identification and expression pattern of miRNAs in wool follicles. Our data might therefore aid in the understanding of the mechanisms of wool follicle development in sheep.     

Identification of the ovine KAP11-1 gene (<Emphasis Type="Italic">KRTAP11</Emphasis>-<Emphasis Type="Italic">1</Emphasis>) and genetic variation in its coding sequence

Keratin-associated proteins (KAPs) are a structural component of the wool fibre and form the matrix between the keratin intermediate filaments (KIFs). The gene encoding high sulphur-protein KAP11-1 has been identified in human, cattle and mouse, but not yet in sheep, despite the economic importance of wool. In this study, PCR using primers based on the cattle KAP11-1 gene sequence produced an amplicon of the expected size with sheep DNA. Upon using PCR–Single Stranded Conformational Polymorphism (PCR–SSCP) analysis in 260 sheep, six different PCR–SSCP patterns were detected. Either one or a combination of two banding patterns was observed for each sheep, suggesting they were either homozygous or heterozygous for this gene. Sequencing of the amplicons confirmed the occurrence of six DNA sequences. All of these were unique, and the greatest homology was with KRTAP11-1 sequences from cattle, human and mouse, suggesting that they were derived from the ovine KAP11-1 gene and were allelic variants. The ovine KAP11-1 gene had an open reading frame of 477 nucleotides encoding 159 amino acids. The putative protein was rich in serine, cysteine, and threonine which account for 18.2–18.9, 12.6 and 12.0 mol%, respectively. Of these, approximately 20 of the serine and threonine residues might be phosphorylated. Five nucleotide substitutions were identified, and one was non-synonymous and would result in an amino acid change at a potential phosphorylation site. The genetic variation found in KRTAP11-1 may influence its expression, protein structure, and/or post-translational modifications, and consequently affect wool fibre structure and wool traits.     

Comparative sequence analysis and radiation hybrid mapping of two epidermal type II keratin genes in the dog: keratin 1 and keratin 2e

In order to extend knowledge of the process of cornification across species and to be better able to recognize inborn errors in keratin synthesis in the dog, we describe the organization and chromosome mapping of canine KRT1 and KRT2E and compare these results to human and murine sequence data. The coding regions of KRT1 and KRT2E are 1,860 bp and 1,902 bp respectively, distributed over nine exons. Both genes are localized on the canine radiation hybrid map to chromosome 27 in the type II keratin gene cluster close to polymorphic markers. These genes are highly conserved across species and based on both genomic and amino acid sequences, canine KRT1 and KRT2E share greater homology with humans than with mice.     

KRT71决定羊驼毛弯曲度的形成

角蛋白71（Keratins 71,KRT71）属于人类Ⅱ型上皮角蛋白,是毛囊特异性的上皮角蛋白基因。相关研究表明,在其他物种中,KRT71与被毛卷曲相关,KRT71在卷曲的被毛形成过程中起着重要的作用。现眼观羊驼背部、耳部和腿部毛发的弯曲程度不同,但KRT71与其被毛的弯曲度是否相关尚不清楚。本研究利用PCR技术克隆KRT71基因全CDS区。通过实时荧光定量PCR技术检测基因的表达。免疫组化、Western 印迹对KRT71蛋白在羊驼背部、耳部和腿部皮肤组织中的表达量进行分析,以探讨KRT71与羊驼毛发弯曲度的关系。结果显示,羊驼的KRT71基因的CDS区共有1 578 bp,编码525个氨基酸;免疫组化结果显示,KRT71在羊驼的背部、耳部和腿部均有表达,并且主要特异性表达于毛囊的内根鞘;实时荧光定量PCR和Western印迹结果显示,KRT71的mRNA和蛋白量均呈现背部﹥腿部﹥耳部的趋势;相较于耳部,背部和腿部的表达量较高。实验结果提示,KRT71的表达量与毛纤维的弯曲度呈正相关,KRT71可能在羊驼毛纤维的弯曲度形成过程中发挥着一定的作用。     

Directed Expression of a Chimeric Type II Keratin Partially Rescues Keratin 5-null Mice

The crucial role of structural support fulfilled by keratin intermediate filaments (IFs) in surface epithelia likely requires that they be organized into cross-linked networks. For IFs comprised of keratins 5 and 14 (K5 and K14), which occur in basal keratinocytes of the epidermis, formation of cross-linked bundles is, in part, self-driven through cis-acting determinants. Here, we targeted the expression of a bundling-competent KRT5/KRT8 chimeric cDNA (KRT8bc) or bundling-deficient wild type KRT8 as a control to the epidermal basal layer of Krt5-null mice to assess the functional importance of keratin IF self-organization in vivo. Such targeted expression of K8bc rescued Krt5-null mice with a 47% frequency, whereas K8 completely failed to do so. This outcome correlated with lower than expected levels of K8bc and especially K8 mRNA and protein in the epidermis of E18.5 replacement embryos. Ex vivo culture of embryonic skin keratinocytes confirmed the ability of K8bc to form IFs in the absence of K5. Additionally, electron microscopy analysis of E18.5 embryonic skin revealed that the striking defects observed in keratin IF bundling, cytoarchitecture, and mitochondria are partially restored by K8bc expression. As young adults, viable KRT8bc replacement mice develop alopecia and chronic skin lesions, indicating that the skin epithelia are not completely normal. These findings are consistent with a contribution of self-mediated organization of keratin IFs to structural support and cytoarchitecture in basal layer keratinocytes of the epidermis and underscore the importance of context-dependent regulation for keratin genes and proteins in vivo.     

Autosomal Recessive Transmission of a Rare KRT74 Variant Causes Hair and Nail Ectodermal Dysplasia: Allelism with Dominant Woolly Hair/Hypotrichosis

Pure hair and nail ectodermal dysplasia (PHNED) comprises a heterogeneous group of rare heritable disorders characterized by brittle hair, hypotrichosis, onychodystrophy and micronychia. Autosomal recessive (AR) PHNED has previously been associated with mutations in either KRT85 or HOXC13 on chromosome 12p11.1-q14.3. We investigated a consanguineous Pakistani family with AR PHNED linked to the keratin gene cluster on 12p11.1 but without detectable mutations in KRT85 and HOXC13. Whole exome sequencing of affected individuals revealed homozygosity for a rare c.821T>C variant (p.Phe274Ser) in the KRT74 gene that segregates AR PHNED in the family. The transition alters the highly conserved Phe274 residue in the coil 1B domain required for long-range dimerization of keratins, suggesting that the mutation compromises the stability of intermediate filaments. Immunohistochemical (IHC) analyses confirmed a strong keratin-74 expression in the nail matrix, the nail bed and the hyponychium of mouse distal digits, as well as in normal human hair follicles. Furthermore, hair follicles and epidermis of an affected family member stained negative for Keratin-74 suggesting a loss of function mechanism mediated by the Phe274Ser substitution. Our observations show for the first time that homozygosity for a KRT74 missense variant may be associated with AR PHNED. Heterozygous KRT74 mutations have previously been associated with autosomal dominant woolly hair/hypotrichosis simplex (ADWH). Thus, our findings expand the phenotypic spectrum associated with KRT74 mutations and imply that a subtype of AR PHNED is allelic with ADWH.     

Polymorphism of the ovine keratin-associated protein 1-4 gene (<Emphasis Type="Italic">KRTAP1-4</Emphasis>)

Keratin-associated proteins (KAPs) are one of the main structural components of the wool fibre and form a semi-rigid matrix in which the keratin intermediate filaments are embedded. Variation in the KAP genes may affect the structure of KAPs and hence wool characteristics. In this study, we used PCR-SSCP to analyse ovine KRTAP1-4 (previously B2D), a gene encoding a member of the KAP1-x family. Nine different PCR-SSCP patterns were detected in the 320 sheep that were analysed. Either one or a combination of two patterns was observed for each sheep, which was consistent with these sheep being either homozygous or heterozygous for this gene. DNA sequencing revealed that these patterns represent nine different DNA sequences. All of these sequences were unique, but shared a high homology with the published ovine KRTAP1-4 sequence, suggesting that these sequences represent allelic variants of KRTAP1-4. There were a total of 14 single nucleotide polymorphisms (SNPs) identified and these SNPs tended to be clustered in two regions. Of the 13 SNPs found in the coding region, nine were non-synonymous SNPs and would result in amino acid changes. The variation detected here may have an impact on the structure of KAP1-4 and hence affect wool traits.     

Genetic and biochemical aspects of keratin synthesis by hair follicles

In this review article the data about synthesis and gene regulation of keratin by hair follicles have been summarized. It has been shown that both differentiation of hair follicle matrix cells and normal growth of hair require the coordinated activities of the genes encoding structural proteins. The keratin genes are clustered in families and are usually 5-10 kb in the genome. The separate clusters of two keratin IF gene families and five KAP gene families have been discovered and some of them have been mapped. The close relation between these clusters suggests that the "global" regulatory domains might govern their expression.     

The transcriptome of early GGT/KRT19-positive hepatocellular carcinoma reveals a downregulated gene expression profile associated with fatty acid metabolism

Hepatocellular carcinoma expressing hepatobiliary progenitor markers, is considered of poor prognosis. By using a hepatocarcinogenesis model, laser capture microdissection, and RNA-Sequencing analysis, we identified an expression profile in GGT/KRT19-positive experimental tumors; 438 differentially expressed genes were found in early and late nodules along with increased collagen deposition. Dysregulated genes were involved in Fatty Acid Metabolism, RXR function, and Hepatic Stellate Cells Activation. Downregulation of Slc27a5, Acsl1, and Cyp2e1, demonstrated that Retinoid X Receptor α (RXRα) function is compromised in GGT/KRT19-positive nodules. Since RXRα controls NRF2 pathway activation, we determined the expression of NRF2 targeted genes; Akr1b8, Akr7a3, Gstp1, Abcc3, Ptgr1, and Txnrd1 were upregulated, indicating NRF2 pathway activation. A comparative analysis in human HCC showed that SLC27A5, ACSL1, CYP2E1, and RXRα gene expression is mutually exclusive with KRT19 gene expression. Our results indicate that the downregulation of Slc27a5, Acsl1, Rxrα, and Cyp2e1 genes is an early event within GGT/KRT19-positive HCC.     

Genetic diversity of selected genes that are potentially economically important in feral sheep of New Zealand

Background

Feral sheep are considered to be a source of genetic variation that has been lost from their domestic counterparts through selection.

Methods

This study investigates variation in the genes KRTAP1-1, KRT33, ADRB3 and DQA2 in Merino-like feral sheep populations from New Zealand and its offshore islands. These genes have previously been shown to influence wool, lamb survival and animal health.

Results

All the genes were polymorphic, but no new allele was identified in the feral populations. In some of these populations, allele frequencies differed from those observed in commercial Merino sheep and other breeds found in New Zealand. Heterozygosity levels were comparable to those observed in other studies on feral sheep. Our results suggest that some of the feral populations may have been either inbred or outbred over the duration of their apparent isolation.

Conclusion

The variation described here allows us to draw some conclusions about the likely genetic origin of the populations and selective pressures that may have acted upon them, but they do not appear to be a source of new genetic material, at least for these four genes.     

Expression of basal cell keratin 15 and keratin 19 in oral squamous neoplasms represents diverse pathophysiologies

Human epithelium contains keratin, which is expressed during differentiation. Depending on the target cell type, different types of keratin are expressed, and their alterations seem to represent changes in cell properties. The basal cells of oral epithelium express keratin 5 (K5), K14, K15 and K19, but their alterations in tumors are unclear. To address this issue and to seek possible diagnostic application, we examined the expression of these keratins in oral squamous cell carcinoma (OSCC) and squamous intraepithelial neoplasm (SIN). cDNA microarray analysis of 43 OSCC revealed slight upregulation of KRT14, downregulation of KRT15 and KRT19, and unaltered KRT5 expression. There were great variations in KRT15 and KRT19 expression across each cancer. Well-differentiated OSCC tended to express more KRT15 and less KRT19 compared to moderately- or poorly-differentiated OSCC. KRT15 was positively correlated with differentiation-related keratin, KRT13. These observations were further investigated by immunohistochemical examination. K5 and K14 were ubiquitously expressed in all 50 OSCC and 50 SIN examined. K15 and K19 were generally downregulated, but were considerably retained in about half of the cases and showed diverse expression patterns. K15-positive cancers tended to show a well-differentiated phenotype, and K19-positive cancers tended to show more invasive tumor fronts. Most K19-positive cancers appeared to develop with little associating SIN. K19 was consistently downregulated in SIN, while K15 was downregulated mainly in high grade SIN. In summary, K15 and K19, unlike K5 or K14, are expressed variably in both SIN and OSCC, which reflects the differences in their pathogenesis and biological behaviors, suggesting their prospective applications as markers for subclassifying OSCC and SIN.     

Genetic and biochemical aspects of the synthesis of keratin by hair follicles

Advances in the area of synthesis and genetic regulation of keratin by the wool-creating structures of the skin, i.e., the hair follicles, is generalized. It is stated that differentiation of the cells of the hair bulb matrix, like normal growth of hair, requires the coordinated action of numerous genes, in particular, the expression of genes associated with synthesis of structural proteins. It is shown that all the keratin genes of the follicle are clustered in families and occupy approximately 5–10 kb in the genome. At the present time certain clusters of two families of IF genes (intermediate hair proteins) along with five families of KAR genes (keratin-associated proteins) have been mapped. The close relations that exist between these clusters give us a basis for claiming that “global” regulator domains are capable of regulating their expression.     

Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments

Background

Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural hair shaft proteins, are largely responsible for hair variation.

Results

We exhaustively characterized the KRTAP gene family in 22 mammalian genomes, confirming the existence of 30 KRTAP subfamilies evolving at different rates with varying degrees of diversification and homogenization. Within the two major classes of KRTAPs, the high cysteine (HS) subfamily experienced strong concerted evolution, high rates of gene conversion/recombination and high GC content. In contrast, high glycine-tyrosine (HGT) KRTAPs showed evidence of positive selection and low rates of gene conversion/recombination. Species with more hair and of higher complexity tended to have more KRATP genes (gene expansion). The sloth, with long and coarse hair, had the most KRTAP genes (175 with 141 being intact). By contrast, the “hairless” dolphin had 35 KRTAPs and the highest pseudogenization rate (74% relative to the 19% mammalian average). Unique hair-related phenotypes, such as scales (armadillo) and spines (hedgehog), were correlated with changes in KRTAPs. Gene expression variation probably also influences hair diversification patterns, for example human have an identical KRTAP repertoire as apes, but much less hair.

Conclusions

We hypothesize that differences in KRTAP gene repertoire and gene expression, together with distinct rates of gene conversion/recombination, pseudogenization and positive selection, are likely responsible for micro and macro-phenotypic hair diversification among mammals in response to adaptations to ecological pressures.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-779) contains supplementary material, which is available to authorized users.     

Discovery of a novel murine keratin 6 (K6) isoform explains the absence of hair and nail defects in mice deficient for K6a and K6b

The murine genome is known to have two keratin 6 (K6) genes, mouse K6 (MK6)a and MK6b. These genes display a complex expression pattern with constitutive expression in the epithelia of oral mucosa, hair follicles, and nail beds. We generated mice deficient for both genes through embryonic stem cell technology. The majority of MK6a/b-/- mice die of starvation within the first two weeks of life. This is due to a localized disintegration of the dorsal tongue epithelium, which results in the build up of a plaque of cell debris that severely impairs feeding. However, approximately 25% of MK6a/b-/- mice survive to adulthood. Remarkably, the surviving MK6a/b-/- mice have normal hair and nails. To our surprise, we discovered MK6 staining both in the hair follicle and the nail bed of MK6a/b-/- mice, indicating the presence of a third MK6 gene. We cloned this previously unknown murine keratin gene and found it to be highly homologous to human K6hf, which is expressed in hair follicles. We therefore termed this gene MK6 hair follicle (MK6hf). The presence of MK6hf in the MK6a/b-/- follicles and nails offers an explanation for the absence of hair and nail defects in MK6a/b-/- animals.     

Primordial follicle assembly was regulated by notch signaling pathway in the mice

Notch signaling pathway, a highly conserved cell signaling system, exists in most multicellular organisms. The objective of this study was to examine Notch signaling pathway in germ cell cyst breakdown and primordial follicle formation. The receptor and ligand genes of Notch pathway (Notch1, Notch2, Jagged1, Jagged2 and Hes1) were extremely down-regulated after newborn mouse ovaries were cultured then exposed to DAPT or L-685,458 in vitro (P < 0.01). Since DAPT or L-685,548 inhibits Notch signaling pathway, the expression of protein LHX8 and NOBOX was significantly reduced during the formation of the primordial follicles. Down-regulated mRNA expression of specific genes including Lhx8, Figla, Sohlh2 and Nobox, were also observed. The percentages of female germ cells in germ cell cysts and primordial follicles were counted after culture of newborn ovaries for 3 days in vitro. The result showed female germ cells in cysts was remarkably up-regulated while as the oocytes in primordial follicles was significantly down-regulated (P < 0.05). In conclusion, Notch signaling pathway may regulate the formation of primordial follicle in mice.