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  • socrates1
Functional roles of Aves class-specific cis-regulatory elements
https://www.nature.com/articles/ncomms14229
Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features
Quote
Abstract
Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers. By analysing 48 bird genomes, we identified millions of avian-specific highly conserved elements (ASHCEs) that predominantly (>99%) reside in non-coding regions. Many ASHCEs show differential histone modifications that may participate in regulation of limb development. Comparative embryonic gene expression analyses across tetrapod species suggest ASHCE-associated genes have unique roles in developing avian limbs. In particular, we demonstrate how the ASHCE driven avian-specific expression of gene Sim1 driven by ASHCE may be associated with the evolution and development of flight feathers. Together, these findings demonstrate regulatory roles of ASHCEs in the creation of avian-specific traits, and further highlight the importance of cis-regulatory rewiring during macroevolutionary changes.

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #1
This is interesting from a few points of view.
One is the role of non-coding sequences:
Quote
The preferential targets of strong purifying selection are usually on protein-coding regions9, for example, 17.55% of HCEs lie within coding regions, some three-fold higher than the percentage of coding regions in whole genome (Fig. 1c). We were therefore surprised to observe, that the proportion of ASHCEs [avian-specific highly conserved elements] that lie within coding regions was ca. 50-fold lower (0.31%, Fig. 1c). The predominance of non-coding sequences within lineage-specific HCEs seems to be a distinguishing feature for the avian lineage, as mammalian-specific HCEs identified using the same method consist of a higher fraction of coding sequences (4.1%; Supplementary Table 5). This result corroborates the above observation that very few lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes. It provides strong evidence to support the recent hypothesis that the principal evolutionary changes might be governed by complex non-coding regulatory networks14.


  • Last Edit: November 28, 2017, 08:10:21 AM by socrates1

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #2

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #3
looks like someone doesn't know about the cis-regulatory hypothesis.

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #4
Quote
We were therefore surprised to observe, that the proportion of ASHCEs [avian-specific highly conserved elements] that lie within coding regions was ca. 50-fold lower

By analysing 48 bird genomes, we identified millions of avian-specific highly conserved elements (ASHCEs) that predominantly (>99%) reside in non-coding regions.

The predominance of non-coding sequences within lineage-specific HCEs seems to be a distinguishing feature for the avian lineage

This result corroborates the above observation that very few lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.

What conclusions if any can be drawn from this "surprising" evidence?

It would seem that avian-specific highly conserved elements (ASHCEs) evolved much more by "changes in non-coding regulatory sequences" than by "the acquisition of novel protein-coding genes."

In fact:
Quote
By analysing 48 bird genomes, we identified millions of avian-specific highly conserved elements (ASHCEs) that predominantly (>99%) reside in non-coding regions.
AND
very few lineage-specific genes emerged in the avian genome

For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
The genome of an organism contains anywhere from a few hundred to thousands of different genes, all encoding a singular product or more. For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed. The most efficient way for an organism to regulate genetic expression is at the transcriptional level. CREs function to control transcription by acting nearby or within a gene. The most well characterized types of CREs are enhancers and promoters. Both of these sequence elements are structural regions of DNA that serve as transcriptional regulators.




  • Last Edit: November 28, 2017, 09:27:38 AM by socrates1

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #5
Quote
We were therefore surprised to observe, that the proportion of ASHCEs [avian-specific highly conserved elements] that lie within coding regions was ca. 50-fold lower

By analysing 48 bird genomes, we identified millions of avian-specific highly conserved elements (ASHCEs) that predominantly (>99%) reside in non-coding regions.

The predominance of non-coding sequences within lineage-specific HCEs seems to be a distinguishing feature for the avian lineage

This result corroborates the above observation that very few lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.

What conclusions if any can be drawn from this "surprising" evidence?

It would seem that avian-specific highly conserved elements (ASHCEs) evolved much more by "changes in non-coding regulatory sequences" than by "the acquisition of novel protein-coding genes."

In fact:
Quote
By analysing 48 bird genomes, we identified millions of avian-specific highly conserved elements (ASHCEs) that predominantly (>99%) reside in non-coding regions.
AND
very few lineage-specific genes emerged in the avian genome

For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
The genome of an organism contains anywhere from a few hundred to thousands of different genes, all encoding a singular product or more. For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed. The most efficient way for an organism to regulate genetic expression is at the transcriptional level. CREs function to control transcription by acting nearby or within a gene. The most well characterized types of CREs are enhancers and promoters. Both of these sequence elements are structural regions of DNA that serve as transcriptional regulators.

It is noteworthy that this is not common. It is surprising:
Quote
We were therefore surprised to observe, that the proportion of ASHCEs [avian-specific highly conserved elements] that lie within coding regions was ca. 50-fold lower
  • Last Edit: November 28, 2017, 09:58:07 AM by socrates1

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #6
ATTN Admins:  ARSE is leaking.
While you were getting your PhD in virology, I got my PhD in truth detection. :wave:  Dave Hawkins

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #7
For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed.
  • Last Edit: November 28, 2017, 01:39:51 PM by socrates1

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #8
Looks like there is no interest in this.

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #9
you don't understand what cis-regulatory regions are and seem to believe this implies something it doesn't, so what's the point of discussing it with you?

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #10
What an odd comment. I have not said anything about what the evidence implies or does not imply.
What does the (surprising) evidence imply?
  • Last Edit: November 28, 2017, 05:10:55 PM by socrates1

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #11
For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed.
Regulatory genes "have a profound effect on phenotype by altering gene expression". So the regulatory genes for birds "generate phenotypic variance".

And
Quote
very few [protein-coding] lineage-specific genes emerged in the avian genome
  • Last Edit: November 29, 2017, 08:05:12 AM by socrates1

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #12
For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed.
Regulatory genes "have a profound effect on phenotype by altering gene expression". So the regulatory genes for birds "generate phenotypic variance".

And
Quote
very few [protein-coding] lineage-specific genes emerged in the avian genome
Quote
Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers.

The (surprising) evidence explains the phenotypes, but does it explain the "numerous evolutionary innovations"?

From the study:
Quote
This result implies that innovation of protein-coding genes might not play a large role in the processes underlying the transitions from dinosaur to the bird lineage.

This result corroborates the above observation that very few lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
  • Last Edit: November 29, 2017, 08:50:39 AM by socrates1

  • Faid
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #13
The (surprising) evidence explains the phenotypes, but does it explain the "numerous evolutionary innovations"?


Why not?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #14
For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed.
Regulatory genes "have a profound effect on phenotype by altering gene expression". So the regulatory genes for birds "generate phenotypic variance".

And
Quote
very few [protein-coding] lineage-specific genes emerged in the avian genome
Quote
Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers.

The (surprising) evidence explains the phenotypes, but does it explain the "numerous evolutionary innovations"?

From the study:
Quote
This result implies that innovation of protein-coding genes might not play a large role in the processes underlying the transitions from dinosaur to the bird lineage.

This result corroborates the above observation that very few lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
Quote
The preferential targets of strong purifying selection are usually on protein-coding regions9, for example, 17.55% of HCEs lie within coding regions, some three-fold higher than the percentage of coding regions in whole genome (Fig. 1c). We were therefore surprised to observe, that the proportion of ASHCEs that lie within coding regions was ca. 50-fold lower (0.31%, Fig. 1c).
Notice that this is not 50% lower but 50 fold lower.

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #15
OP needs to take a course in basic genetics and another course in developmental biology

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #16
For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed.
Regulatory genes "have a profound effect on phenotype by altering gene expression". So the regulatory genes for birds "generate phenotypic variance".

And
Quote
very few [protein-coding] lineage-specific genes emerged in the avian genome
Quote
Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers.

The (surprising) evidence explains the phenotypes, but does it explain the "numerous evolutionary innovations"?

From the study:
Quote
This result implies that innovation of protein-coding genes might not play a large role in the processes underlying the transitions from dinosaur to the bird lineage.

This result corroborates the above observation that very few lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
Quote
The preferential targets of strong purifying selection are usually on protein-coding regions9, for example, 17.55% of HCEs lie within coding regions, some three-fold higher than the percentage of coding regions in whole genome (Fig. 1c). We were therefore surprised to observe, that the proportion of ASHCEs that lie within coding regions was ca. 50-fold lower (0.31%, Fig. 1c).
Notice that this is not 50% lower but 50 fold lower.
This is so far outside the usual that it calls for some kind of explanation.

  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #17
Mods:
Self-quoting monologs ignoring all input from others do not belong in Science Discussion Forum.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #18
Notice that there is no input from others.
Insults do not count.

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #19
For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed.
Regulatory genes "have a profound effect on phenotype by altering gene expression". So the regulatory genes for birds "generate phenotypic variance".

And
Quote
very few [protein-coding] lineage-specific genes emerged in the avian genome
Quote
Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers.

The (surprising) evidence explains the phenotypes, but does it explain the "numerous evolutionary innovations"?

From the study:
Quote
This result implies that innovation of protein-coding genes might not play a large role in the processes underlying the transitions from dinosaur to the bird lineage.

This result corroborates the above observation that very few lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
Quote
The preferential targets of strong purifying selection are usually on protein-coding regions9, for example, 17.55% of HCEs lie within coding regions, some three-fold higher than the percentage of coding regions in whole genome (Fig. 1c). We were therefore surprised to observe, that the proportion of ASHCEs that lie within coding regions was ca. 50-fold lower (0.31%, Fig. 1c).
Notice that this is not 50% lower but 50 fold lower.
This is so far outside the usual that it calls for some kind of explanation.
If others here want a discussion why not start by offering up a possible explanation for this.

  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #20
The (surprising) evidence explains the phenotypes, but does it explain the "numerous evolutionary innovations"?


Why not?
^^^^  "Why not?"  is not an insult.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #21
Cis-regulatory hypothesis. Everyone who is anyone is pretty much already aware that a vast majority of loci associated with morphological evolution are regulatory rather than functional changes in the genes themselves. Hell, even a majority of major mutations (e.g. the antennapedia Drosophila mutant) are actually changes in relationships between regulatory regions and actual gene exons. This is not actually surprising at all for anyone working in the field.

  • Faid
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #22
Notice that there is no input from others.
Insults do not count.
The (surprising) evidence explains the phenotypes, but does it explain the "numerous evolutionary innovations"?


Why not?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #23
For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed.
Regulatory genes "have a profound effect on phenotype by altering gene expression". So the regulatory genes for birds "generate phenotypic variance".

And
Quote
very few [protein-coding] lineage-specific genes emerged in the avian genome
Quote
Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers.

The (surprising) evidence explains the phenotypes, but does it explain the "numerous evolutionary innovations"?

From the study:
Quote
This result implies that innovation of protein-coding genes might not play a large role in the processes underlying the transitions from dinosaur to the bird lineage.

This result corroborates the above observation that very few lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
Quote
The preferential targets of strong purifying selection are usually on protein-coding regions9, for example, 17.55% of HCEs lie within coding regions, some three-fold higher than the percentage of coding regions in whole genome (Fig. 1c). We were therefore surprised to observe, that the proportion of ASHCEs that lie within coding regions was ca. 50-fold lower (0.31%, Fig. 1c).
Notice that this is not 50% lower but 50 fold lower.
This is so far outside the usual that it calls for some kind of explanation.
If others here want a discussion why not start by offering up a possible explanation for this.
So no explanation as to why the avian situation is so outside the usual.
  • Last Edit: November 29, 2017, 12:21:04 PM by socrates1

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #24
For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed.
Regulatory genes "have a profound effect on phenotype by altering gene expression". So the regulatory genes for birds "generate phenotypic variance".

And
Quote
very few [protein-coding] lineage-specific genes emerged in the avian genome
Quote
Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers.

The (surprising) evidence explains the phenotypes, but does it explain the "numerous evolutionary innovations"?

From the study:
Quote
This result implies that innovation of protein-coding genes might not play a large role in the processes underlying the transitions from dinosaur to the bird lineage.

This result corroborates the above observation that very few lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
Quote
The preferential targets of strong purifying selection are usually on protein-coding regions9, for example, 17.55% of HCEs lie within coding regions, some three-fold higher than the percentage of coding regions in whole genome (Fig. 1c). We were therefore surprised to observe, that the proportion of ASHCEs that lie within coding regions was ca. 50-fold lower (0.31%, Fig. 1c).
Notice that this is not 50% lower but 50 fold lower.
This is so far outside the usual that it calls for some kind of explanation.
If others here want a discussion why not start by offering up a possible explanation for this.
So no explanation as to why the avian situation is so outside the usual.

Whims of the Quantum Engineers?   :dunno:
While you were getting your PhD in virology, I got my PhD in truth detection. :wave:  Dave Hawkins