Limits...
Roles of the developmental regulator unc-62/Homothorax in limiting longevity in Caenorhabditis elegans.

Van Nostrand EL, Sánchez-Blanco A, Wu B, Nguyen A, Kim SK - PLoS Genet. (2013)

Bottom Line: Through analysis of the downstream consequences of unc-62 knockdown, we identify multiple effects linked to aging.Second, unc-62 RNAi results in a broad increase in expression of intestinal genes that typically decrease expression with age, suggesting that unc-62 activity balances intestinal resource allocation between yolk protein expression and fertility on the one hand and somatic functions on the other.These results illustrate how unc-62 regulation of intestinal gene expression is responsible for limiting lifespan during the normal aging process.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Stanford University Medical Center, Stanford, California, USA.

ABSTRACT
The normal aging process is associated with stereotyped changes in gene expression, but the regulators responsible for these age-dependent changes are poorly understood. Using a novel genomics approach, we identified HOX co-factor unc-62 (Homothorax) as a developmental regulator that binds proximal to age-regulated genes and modulates lifespan. Although unc-62 is expressed in diverse tissues, its functions in the intestine play a particularly important role in modulating lifespan, as intestine-specific knockdown of unc-62 by RNAi increases lifespan. An alternatively-spliced, tissue-specific isoform of unc-62 is expressed exclusively in the intestine and declines with age. Through analysis of the downstream consequences of unc-62 knockdown, we identify multiple effects linked to aging. First, unc-62 RNAi decreases the expression of yolk proteins (vitellogenins) that aggregate in the body cavity in old age. Second, unc-62 RNAi results in a broad increase in expression of intestinal genes that typically decrease expression with age, suggesting that unc-62 activity balances intestinal resource allocation between yolk protein expression and fertility on the one hand and somatic functions on the other. Finally, in old age, the intestine shows increased expression of several aberrant genes; these UNC-62 targets are expressed predominantly in neuronal cells in developing animals, but surprisingly show increased expression in the intestine of old animals. Intestinal expression of some of these genes during aging is detrimental for longevity; notably, increased expression of insulin ins-7 limits lifespan by repressing activity of insulin pathway response factor DAF-16/FOXO in aged animals. These results illustrate how unc-62 regulation of intestinal gene expression is responsible for limiting lifespan during the normal aging process.

Show MeSH
Identification of direct and regulated targets of UNC-62 in adults by ChIP–seq and RNA–seq.(A) An example of UNC-62 ChIP-seq read density at a significantly enriched binding site is shown. Top tracks show read density in ChIP-seq experiments for UNC-62 in young adults (green) and L3 larvae (blue) as well as non-immunoprecipitated input control (grey). Boxes underneath the read density tracks indicate significant binding sites (q-value≤10−5). Bottom tracks indicate genes (with coding exons in thick blue boxes). (B) Examples of unc-62 RNAi 3′-end enriched RNA-seq data is shown. We performed three independent experiments in which we fed worms either unc-62 RNAi or control bacteria, isolated mRNA and generated RNA-seq libraries, and sequenced these libraries on the Illumina HiSeq platform. For the ilys-5 (left) and vit-2 (right) genomic regions, reads map to annotated exon regions on the proper strand, and are enriched at the 3′ end of the transcript. Read densities are displayed for control (black) and unc-62 RNAi (blue), scaled as reads per million uniquely mapping reads. (C) Rank Products-based analysis (based on [27]; see Methods and Figure S5) to identify genes reproducibly altered across all three biological replicates identified 67 genes significantly increased and 115 genes significantly decreased upon unc-62 RNAi at a 10% false positive rate.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3585033&req=5

pgen-1003325-g004: Identification of direct and regulated targets of UNC-62 in adults by ChIP–seq and RNA–seq.(A) An example of UNC-62 ChIP-seq read density at a significantly enriched binding site is shown. Top tracks show read density in ChIP-seq experiments for UNC-62 in young adults (green) and L3 larvae (blue) as well as non-immunoprecipitated input control (grey). Boxes underneath the read density tracks indicate significant binding sites (q-value≤10−5). Bottom tracks indicate genes (with coding exons in thick blue boxes). (B) Examples of unc-62 RNAi 3′-end enriched RNA-seq data is shown. We performed three independent experiments in which we fed worms either unc-62 RNAi or control bacteria, isolated mRNA and generated RNA-seq libraries, and sequenced these libraries on the Illumina HiSeq platform. For the ilys-5 (left) and vit-2 (right) genomic regions, reads map to annotated exon regions on the proper strand, and are enriched at the 3′ end of the transcript. Read densities are displayed for control (black) and unc-62 RNAi (blue), scaled as reads per million uniquely mapping reads. (C) Rank Products-based analysis (based on [27]; see Methods and Figure S5) to identify genes reproducibly altered across all three biological replicates identified 67 genes significantly increased and 115 genes significantly decreased upon unc-62 RNAi at a 10% false positive rate.

Mentions: In addition to the adult ChIP-seq targets described earlier, we analyzed UNC-62 ChIP-seq targets identified in the earlier L3 larval stage, when unc-62 appears predominantly as the 7b isoform (E.V.N. and S.K.K. unpublished data). In the L3 stage, the ChIP seq experiments identified 1193 UNC-62 binding sites, of which 251 are factor-specific. However, many young adult UNC-62 binding sites showed little enrichment in the L3 stage ChIP-seq experiment (Figure 4A and E.V.N. and S.K.K. unpublished data). We compared the 151 genes associated with these UNC-62 L3 binding sites to the set of aging-regulated genes and found only 10 UNC-62 L3 targets that are also age-dependent, which is not significantly enriched (.98-fold, p>.1). Thus, although the adult UNC-62 targets tend to be differentially expressed with age, the UNC-62 targets in L3 larvae are not. The genes bound by UNC-62 also have differential tissue-specificity: L3 larval targets are enriched for neuronal-enriched expression, whereas young adult targets are instead enriched for intestine-specific expression (E.V.N. and S.K.K. unpublished data). These distinctions corresponds to the pattern of alternative splicing of UNC-62; i.e., up until the L3 stage unc-62 is expressed predominantly as the unc-62(7b) isoform in neurons and the hypodermis, whereas in adults unc-62 appears as the unc-62(7a) isoform in the intestine and as the unc-62(7b) isoform elsewhere (E.V.N. and S.K.K. unpublished data). We focused our analysis on the young adult targets as these targets are enriched for genes with age-dependent expression.


Roles of the developmental regulator unc-62/Homothorax in limiting longevity in Caenorhabditis elegans.

Van Nostrand EL, Sánchez-Blanco A, Wu B, Nguyen A, Kim SK - PLoS Genet. (2013)

Identification of direct and regulated targets of UNC-62 in adults by ChIP–seq and RNA–seq.(A) An example of UNC-62 ChIP-seq read density at a significantly enriched binding site is shown. Top tracks show read density in ChIP-seq experiments for UNC-62 in young adults (green) and L3 larvae (blue) as well as non-immunoprecipitated input control (grey). Boxes underneath the read density tracks indicate significant binding sites (q-value≤10−5). Bottom tracks indicate genes (with coding exons in thick blue boxes). (B) Examples of unc-62 RNAi 3′-end enriched RNA-seq data is shown. We performed three independent experiments in which we fed worms either unc-62 RNAi or control bacteria, isolated mRNA and generated RNA-seq libraries, and sequenced these libraries on the Illumina HiSeq platform. For the ilys-5 (left) and vit-2 (right) genomic regions, reads map to annotated exon regions on the proper strand, and are enriched at the 3′ end of the transcript. Read densities are displayed for control (black) and unc-62 RNAi (blue), scaled as reads per million uniquely mapping reads. (C) Rank Products-based analysis (based on [27]; see Methods and Figure S5) to identify genes reproducibly altered across all three biological replicates identified 67 genes significantly increased and 115 genes significantly decreased upon unc-62 RNAi at a 10% false positive rate.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585033&req=5

pgen-1003325-g004: Identification of direct and regulated targets of UNC-62 in adults by ChIP–seq and RNA–seq.(A) An example of UNC-62 ChIP-seq read density at a significantly enriched binding site is shown. Top tracks show read density in ChIP-seq experiments for UNC-62 in young adults (green) and L3 larvae (blue) as well as non-immunoprecipitated input control (grey). Boxes underneath the read density tracks indicate significant binding sites (q-value≤10−5). Bottom tracks indicate genes (with coding exons in thick blue boxes). (B) Examples of unc-62 RNAi 3′-end enriched RNA-seq data is shown. We performed three independent experiments in which we fed worms either unc-62 RNAi or control bacteria, isolated mRNA and generated RNA-seq libraries, and sequenced these libraries on the Illumina HiSeq platform. For the ilys-5 (left) and vit-2 (right) genomic regions, reads map to annotated exon regions on the proper strand, and are enriched at the 3′ end of the transcript. Read densities are displayed for control (black) and unc-62 RNAi (blue), scaled as reads per million uniquely mapping reads. (C) Rank Products-based analysis (based on [27]; see Methods and Figure S5) to identify genes reproducibly altered across all three biological replicates identified 67 genes significantly increased and 115 genes significantly decreased upon unc-62 RNAi at a 10% false positive rate.
Mentions: In addition to the adult ChIP-seq targets described earlier, we analyzed UNC-62 ChIP-seq targets identified in the earlier L3 larval stage, when unc-62 appears predominantly as the 7b isoform (E.V.N. and S.K.K. unpublished data). In the L3 stage, the ChIP seq experiments identified 1193 UNC-62 binding sites, of which 251 are factor-specific. However, many young adult UNC-62 binding sites showed little enrichment in the L3 stage ChIP-seq experiment (Figure 4A and E.V.N. and S.K.K. unpublished data). We compared the 151 genes associated with these UNC-62 L3 binding sites to the set of aging-regulated genes and found only 10 UNC-62 L3 targets that are also age-dependent, which is not significantly enriched (.98-fold, p>.1). Thus, although the adult UNC-62 targets tend to be differentially expressed with age, the UNC-62 targets in L3 larvae are not. The genes bound by UNC-62 also have differential tissue-specificity: L3 larval targets are enriched for neuronal-enriched expression, whereas young adult targets are instead enriched for intestine-specific expression (E.V.N. and S.K.K. unpublished data). These distinctions corresponds to the pattern of alternative splicing of UNC-62; i.e., up until the L3 stage unc-62 is expressed predominantly as the unc-62(7b) isoform in neurons and the hypodermis, whereas in adults unc-62 appears as the unc-62(7a) isoform in the intestine and as the unc-62(7b) isoform elsewhere (E.V.N. and S.K.K. unpublished data). We focused our analysis on the young adult targets as these targets are enriched for genes with age-dependent expression.

Bottom Line: Through analysis of the downstream consequences of unc-62 knockdown, we identify multiple effects linked to aging.Second, unc-62 RNAi results in a broad increase in expression of intestinal genes that typically decrease expression with age, suggesting that unc-62 activity balances intestinal resource allocation between yolk protein expression and fertility on the one hand and somatic functions on the other.These results illustrate how unc-62 regulation of intestinal gene expression is responsible for limiting lifespan during the normal aging process.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Stanford University Medical Center, Stanford, California, USA.

ABSTRACT
The normal aging process is associated with stereotyped changes in gene expression, but the regulators responsible for these age-dependent changes are poorly understood. Using a novel genomics approach, we identified HOX co-factor unc-62 (Homothorax) as a developmental regulator that binds proximal to age-regulated genes and modulates lifespan. Although unc-62 is expressed in diverse tissues, its functions in the intestine play a particularly important role in modulating lifespan, as intestine-specific knockdown of unc-62 by RNAi increases lifespan. An alternatively-spliced, tissue-specific isoform of unc-62 is expressed exclusively in the intestine and declines with age. Through analysis of the downstream consequences of unc-62 knockdown, we identify multiple effects linked to aging. First, unc-62 RNAi decreases the expression of yolk proteins (vitellogenins) that aggregate in the body cavity in old age. Second, unc-62 RNAi results in a broad increase in expression of intestinal genes that typically decrease expression with age, suggesting that unc-62 activity balances intestinal resource allocation between yolk protein expression and fertility on the one hand and somatic functions on the other. Finally, in old age, the intestine shows increased expression of several aberrant genes; these UNC-62 targets are expressed predominantly in neuronal cells in developing animals, but surprisingly show increased expression in the intestine of old animals. Intestinal expression of some of these genes during aging is detrimental for longevity; notably, increased expression of insulin ins-7 limits lifespan by repressing activity of insulin pathway response factor DAF-16/FOXO in aged animals. These results illustrate how unc-62 regulation of intestinal gene expression is responsible for limiting lifespan during the normal aging process.

Show MeSH