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A large family of Dscam genes with tandemly arrayed 5' cassettes in Chelicerata.

Yue Y, Meng Y, Ma H, Hou S, Cao G, Hong W, Shi Y, Guo P, Liu B, Shi F, Yang Y, Jin Y - Nat Commun (2016)

Bottom Line: Furthermore, extraordinary isoform diversity has been generated through a combination of alternating promoter and alternative splicing.These sDscams have a high sequence similarity with Drosophila Dscam1, and share striking organizational resemblance to the 5' variable regions of vertebrate clustered Pcdhs.Hence, our findings have important implications for understanding the functional similarities between Drosophila Dscam1 and vertebrate Pcdhs, and may provide further mechanistic insights into the regulation of isoform diversity.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China.

ABSTRACT
Drosophila Dscam1 (Down Syndrome Cell Adhesion Molecules) and vertebrate clustered protocadherins (Pcdhs) are two classic examples of the extraordinary isoform diversity from a single genomic locus. Dscam1 encodes 38,016 distinct isoforms via mutually exclusive splicing in D. melanogaster, while the vertebrate clustered Pcdhs utilize alternative promoters to generate isoform diversity. Here we reveal a shortened Dscam gene family with tandemly arrayed 5' cassettes in Chelicerata. These cassette repeats generally comprise two or four exons, corresponding to variable Immunoglobulin 7 (Ig7) or Ig7-8 domains of Drosophila Dscam1. Furthermore, extraordinary isoform diversity has been generated through a combination of alternating promoter and alternative splicing. These sDscams have a high sequence similarity with Drosophila Dscam1, and share striking organizational resemblance to the 5' variable regions of vertebrate clustered Pcdhs. Hence, our findings have important implications for understanding the functional similarities between Drosophila Dscam1 and vertebrate Pcdhs, and may provide further mechanistic insights into the regulation of isoform diversity.

No MeSH data available.


Related in: MedlinePlus

Expression analysis of 5′ variable exons of M. martensii sDscam.(a) Relative expression levels of sDscamα and sDscamβ1–6 transcripts in different tissues. The expression level for each transcript is shown as reads per million (r.p.m.) of its corresponding constitutive exons. Data are expressed as a percentage of the mean±s.d. from two independent experiments. (b) The relative inclusion frequency of the sDscamα variable exon in different tissues. Alternative exon 2 was selected to calculate the level of expression. (c) The relative frequency of the variable exon clusters of sDscamβ1–6. Variable cassette 4 of sDscamβ1 was abundantly expressed in the cephalothorax (shown as the black arrow), but was barely detectable in other tissues. sDscamβ3 variable cassette 11 was abundantly expressed in the poison gland (shown as the blue arrow), but was barely detectable in other tissues. The 25-nt fragmented RNA-seq data sets were mapped to calculate the relative expression level. These results based on 25-nucleotide (nt) mapping were consistent with those based on 50-nt mapping, except for some very lowly expressed tissues (Supplementary Fig. 7).
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f3: Expression analysis of 5′ variable exons of M. martensii sDscam.(a) Relative expression levels of sDscamα and sDscamβ1–6 transcripts in different tissues. The expression level for each transcript is shown as reads per million (r.p.m.) of its corresponding constitutive exons. Data are expressed as a percentage of the mean±s.d. from two independent experiments. (b) The relative inclusion frequency of the sDscamα variable exon in different tissues. Alternative exon 2 was selected to calculate the level of expression. (c) The relative frequency of the variable exon clusters of sDscamβ1–6. Variable cassette 4 of sDscamβ1 was abundantly expressed in the cephalothorax (shown as the black arrow), but was barely detectable in other tissues. sDscamβ3 variable cassette 11 was abundantly expressed in the poison gland (shown as the blue arrow), but was barely detectable in other tissues. The 25-nt fragmented RNA-seq data sets were mapped to calculate the relative expression level. These results based on 25-nucleotide (nt) mapping were consistent with those based on 50-nt mapping, except for some very lowly expressed tissues (Supplementary Fig. 7).

Mentions: To determine the expression profiles of the variable cassettes in M. martensii sDscams, paired-end sequencing of poly(A)-tailed transcripts was performed on five dissected adult tissue samples, including the cephalothorax, abdomen, muscles, haemocytes and poison glands. RNA-seq reads were mapped to the genome sequence of sDscams as described above. Based on the RNA-seq data of constitutive exons, the sDscamα and sDscamβ1–6 transcripts were differentially expressed (Fig. 3a). The sDscamα and sDscamβ1–6 transcripts were expressed at much higher levels in the cephalothorax than in the abdomen, muscles and haemocytes (Fig. 3a; Supplementary Fig. 7a). This is largely consistent with previous studies in which Dscams were highly expressed in neural tissues1327. Notably, sDscamβ3, sDscamβ5 and sDscamβ6 transcripts were expressed at maximum levels in the poison glands. It would be of interest to know whether the sDscam isoform diversity contributes to immune protection, as previously reported for Dscam1 isoforms in insects27. Transcriptional signals were detected for almost all of the 5′ variable exons of sDscamα and the six sDscamβ genes in at least one of the tissues of M. martensii (Fig. 3b,c; Supplementary Fig. 7b,c). For each sDscam gene, the relative abundance of isoforms differed markedly among the variable exons. For example, the most abundant 10 sDscamα isoforms accounted for 54.7% and 52.5% of all reads from the cephalothorax and abdomen, respectively (Fig. 3b,c). Interestingly, the variable cassettes most distal to the constitutive exons tended to occur less frequently in all tissues for all sDscams, except for sDscamβ4. In sDscamβ2–3 and sDscamβ5–6, the inclusion frequency of a variable exon largely correlated with its proximity to the first constitutive exon (Supplementary Fig. 8a–d).


A large family of Dscam genes with tandemly arrayed 5' cassettes in Chelicerata.

Yue Y, Meng Y, Ma H, Hou S, Cao G, Hong W, Shi Y, Guo P, Liu B, Shi F, Yang Y, Jin Y - Nat Commun (2016)

Expression analysis of 5′ variable exons of M. martensii sDscam.(a) Relative expression levels of sDscamα and sDscamβ1–6 transcripts in different tissues. The expression level for each transcript is shown as reads per million (r.p.m.) of its corresponding constitutive exons. Data are expressed as a percentage of the mean±s.d. from two independent experiments. (b) The relative inclusion frequency of the sDscamα variable exon in different tissues. Alternative exon 2 was selected to calculate the level of expression. (c) The relative frequency of the variable exon clusters of sDscamβ1–6. Variable cassette 4 of sDscamβ1 was abundantly expressed in the cephalothorax (shown as the black arrow), but was barely detectable in other tissues. sDscamβ3 variable cassette 11 was abundantly expressed in the poison gland (shown as the blue arrow), but was barely detectable in other tissues. The 25-nt fragmented RNA-seq data sets were mapped to calculate the relative expression level. These results based on 25-nucleotide (nt) mapping were consistent with those based on 50-nt mapping, except for some very lowly expressed tissues (Supplementary Fig. 7).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835542&req=5

f3: Expression analysis of 5′ variable exons of M. martensii sDscam.(a) Relative expression levels of sDscamα and sDscamβ1–6 transcripts in different tissues. The expression level for each transcript is shown as reads per million (r.p.m.) of its corresponding constitutive exons. Data are expressed as a percentage of the mean±s.d. from two independent experiments. (b) The relative inclusion frequency of the sDscamα variable exon in different tissues. Alternative exon 2 was selected to calculate the level of expression. (c) The relative frequency of the variable exon clusters of sDscamβ1–6. Variable cassette 4 of sDscamβ1 was abundantly expressed in the cephalothorax (shown as the black arrow), but was barely detectable in other tissues. sDscamβ3 variable cassette 11 was abundantly expressed in the poison gland (shown as the blue arrow), but was barely detectable in other tissues. The 25-nt fragmented RNA-seq data sets were mapped to calculate the relative expression level. These results based on 25-nucleotide (nt) mapping were consistent with those based on 50-nt mapping, except for some very lowly expressed tissues (Supplementary Fig. 7).
Mentions: To determine the expression profiles of the variable cassettes in M. martensii sDscams, paired-end sequencing of poly(A)-tailed transcripts was performed on five dissected adult tissue samples, including the cephalothorax, abdomen, muscles, haemocytes and poison glands. RNA-seq reads were mapped to the genome sequence of sDscams as described above. Based on the RNA-seq data of constitutive exons, the sDscamα and sDscamβ1–6 transcripts were differentially expressed (Fig. 3a). The sDscamα and sDscamβ1–6 transcripts were expressed at much higher levels in the cephalothorax than in the abdomen, muscles and haemocytes (Fig. 3a; Supplementary Fig. 7a). This is largely consistent with previous studies in which Dscams were highly expressed in neural tissues1327. Notably, sDscamβ3, sDscamβ5 and sDscamβ6 transcripts were expressed at maximum levels in the poison glands. It would be of interest to know whether the sDscam isoform diversity contributes to immune protection, as previously reported for Dscam1 isoforms in insects27. Transcriptional signals were detected for almost all of the 5′ variable exons of sDscamα and the six sDscamβ genes in at least one of the tissues of M. martensii (Fig. 3b,c; Supplementary Fig. 7b,c). For each sDscam gene, the relative abundance of isoforms differed markedly among the variable exons. For example, the most abundant 10 sDscamα isoforms accounted for 54.7% and 52.5% of all reads from the cephalothorax and abdomen, respectively (Fig. 3b,c). Interestingly, the variable cassettes most distal to the constitutive exons tended to occur less frequently in all tissues for all sDscams, except for sDscamβ4. In sDscamβ2–3 and sDscamβ5–6, the inclusion frequency of a variable exon largely correlated with its proximity to the first constitutive exon (Supplementary Fig. 8a–d).

Bottom Line: Furthermore, extraordinary isoform diversity has been generated through a combination of alternating promoter and alternative splicing.These sDscams have a high sequence similarity with Drosophila Dscam1, and share striking organizational resemblance to the 5' variable regions of vertebrate clustered Pcdhs.Hence, our findings have important implications for understanding the functional similarities between Drosophila Dscam1 and vertebrate Pcdhs, and may provide further mechanistic insights into the regulation of isoform diversity.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China.

ABSTRACT
Drosophila Dscam1 (Down Syndrome Cell Adhesion Molecules) and vertebrate clustered protocadherins (Pcdhs) are two classic examples of the extraordinary isoform diversity from a single genomic locus. Dscam1 encodes 38,016 distinct isoforms via mutually exclusive splicing in D. melanogaster, while the vertebrate clustered Pcdhs utilize alternative promoters to generate isoform diversity. Here we reveal a shortened Dscam gene family with tandemly arrayed 5' cassettes in Chelicerata. These cassette repeats generally comprise two or four exons, corresponding to variable Immunoglobulin 7 (Ig7) or Ig7-8 domains of Drosophila Dscam1. Furthermore, extraordinary isoform diversity has been generated through a combination of alternating promoter and alternative splicing. These sDscams have a high sequence similarity with Drosophila Dscam1, and share striking organizational resemblance to the 5' variable regions of vertebrate clustered Pcdhs. Hence, our findings have important implications for understanding the functional similarities between Drosophila Dscam1 and vertebrate Pcdhs, and may provide further mechanistic insights into the regulation of isoform diversity.

No MeSH data available.


Related in: MedlinePlus