Bacterial RNAs - Revision history

Leandra at 11:15, 22 June 2007

Leandra — Fri, 22 Jun 2007 11:15:53 GMT

←Older revision		Revision as of 11:15, 22 June 2007
Line 3:		Line 3:

	Starting from this considerations we decided to perform a systematic analysis of these elements and to identify		Starting from this considerations we decided to perform a systematic analysis of these elements and to identify
-	all the repeated sequence families able to share a common SLS. The project started with the identification of all the sequences able to fold in a SLS manner from a set of 40 wholly-sequenced genomes representative of ~~whole~~ bacterial world. SLSs were extracted, annotated and stored in a relational database. A first result of this project was to demonstrate that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. ~~So it~~ is ~~probable~~ that there is a selective pressure in some microorganisms to preserve these sequences because of their biological functions.	+	all the repeated sequence families able to share a common SLS. The project started with the identification of all the sequences able to fold in a SLS manner from a set of 40 wholly-sequenced genomes representative of the bacterial world. SLSs were extracted, annotated and stored in a relational database. A first result of this project was to demonstrate that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. It is therefore possible that there is a selective pressure in some microorganisms to preserve these sequences because of their biological functions.
-	A second analysis based on clustering procedures revealed that most of analyzed genomes have SLSs that can be grouped by sequence ~~similarities and~~, ~~interestingly, such SLSs (~~which correspond to a very little fraction of starting population) have a substantially higher aptitude to fold into a stable secondary structure than the initial set.	+	A second analysis based on clustering procedures revealed that most of analyzed genomes have SLSs that can be grouped by sequence similarity. Such SLSs, which correspond to a very little fraction of the starting population, have a substantially higher aptitude to fold into a stable secondary structure than the initial set.
-	This procedure ~~allows~~ to identify a large collection of families of repeated stem-loop containing sequences. Secondary structure analysis~~, then, reveals~~ for many of them the presence of a conserved secondary structure ~~which is likely~~ linked to their biological function.	+	This procedure allowed to identify a large collection of families of repeated stem-loop containing sequences. Secondary structure analysis revealed for many of them the presence of a conserved secondary structure, possibly linked to their biological function.

Luca at 16:50, 20 June 2007

Luca — Wed, 20 Jun 2007 16:50:09 GMT

←Older revision		Revision as of 16:50, 20 June 2007
Line 3:		Line 3:

	Starting from this considerations we decided to perform a systematic analysis of these elements and to identify		Starting from this considerations we decided to perform a systematic analysis of these elements and to identify
-	all the repeated sequence families able to share a common SLS. The project started with the identification of all the sequences able to fold in a SLS manner from a set of 40 wholly-sequenced genomes representative of whole bacterial world. SLSs were extracted, annotated and stored in a relational database. A first result of this project was to demonstrate that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. So it is ~~assumable~~ that there is a selective pressure in some ~~organisms~~ to preserve these sequences which ~~are important~~ for their biological function.	+	all the repeated sequence families able to share a common SLS. The project started with the identification of all the sequences able to fold in a SLS manner from a set of 40 wholly-sequenced genomes representative of whole bacterial world. SLSs were extracted, annotated and stored in a relational database. A first result of this project was to demonstrate that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. So it is probable that there is a selective pressure in some microorganisms to preserve these sequences because of their biological functions.
		+	A second analysis based on clustering procedures revealed that most of analyzed genomes have SLSs that can be grouped by sequence similarities and, interestingly, such SLSs (which correspond to a very little fraction of starting population) have a substantially higher aptitude to fold into a stable secondary structure than the initial set.
		+	This procedure allows to identify a large collection of families of repeated stem-loop containing sequences. Secondary structure analysis, then, reveals for many of them the presence of a conserved secondary structure which is likely linked to their biological function.

-	a large collection of families of repeated stem-loop containing sequences has been identified by clustering stemloop structures according to sequence similarity in the analyzed species. Secondary structure analysis reveals the presence of a large number of sequences where a conserved secondary structure may be demonstrated within the family.
-
-	We performed a first systematic analysis of the distribution of SLSs in and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.
-
-	A second analysis based on clustering procedures revealed that 29 out of 40 analyzed genomes have SLSs that can be grouped by sequence similarities. Such SLSs corresponding to about 1% of the whole population and have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Further refinements led to identify 92 families of repeated sequence, mostly sharing a common SLS. 25 of them include all well-known SLS containing repeats and some families reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions.

	== References ==		== References ==

Luca at 16:39, 20 June 2007

Luca — Wed, 20 Jun 2007 16:39:27 GMT

←Older revision		Revision as of 16:39, 20 June 2007
Line 1:		Line 1:
	[[Image:Bacterial_pae.jpg\|300px\|right\|thumb\|PAE-1 bacterial family secondary structure]]		[[Image:Bacterial_pae.jpg\|300px\|right\|thumb\|PAE-1 bacterial family secondary structure]]
-	Bacterial genomes are generally compact and most of their sequence is involved in protein coding, but a growing number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. Many of these sequences are active as RNA and often contain simple stem-loop structures (SLS), essential to their functionality. ~~Moreover, families of repeated sequences, sharing a common SLS,~~ have been ~~described~~ in ~~many~~ bacterial genomes even if only in few cases a clear biological function was assessed. ~~In order to quantify~~ this ~~phenomenon~~ we ~~performed~~ a systematic analysis of the ~~distribution~~ of ~~SLSs~~ in 40 wholly-sequenced ~~bacterial~~ genomes ~~which are~~ representative of ~~the~~ whole bacterial world. In this ~~way we demonstrated~~ that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition.	+	Bacterial genomes are generally compact and most of their sequence is involved in protein coding, but a growing number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. Many of these sequences are active as RNA and often contain simple stem-loop structures (SLS), essential to their functionality. SLSs have been found also in repetitive sequences in several bacterial genomes, even if only in few cases a clear biological function was assessed.
		+
		+	Starting from this considerations we decided to perform a systematic analysis of these elements and to identify
		+	all the repeated sequence families able to share a common SLS. The project started with the identification of all the sequences able to fold in a SLS manner from a set of 40 wholly-sequenced genomes representative of whole bacterial world. SLSs were extracted, annotated and stored in a relational database. A first result of this project was to demonstrate that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. So it is assumable that there is a selective pressure in some organisms to preserve these sequences which are important for their biological function.
		+
	a large collection of families of repeated stem-loop containing sequences has been identified by clustering stemloop structures according to sequence similarity in the analyzed species. Secondary structure analysis reveals the presence of a large number of sequences where a conserved secondary structure may be demonstrated within the family.		a large collection of families of repeated stem-loop containing sequences has been identified by clustering stemloop structures according to sequence similarity in the analyzed species. Secondary structure analysis reveals the presence of a large number of sequences where a conserved secondary structure may be demonstrated within the family.

-	We performed a first systematic analysis of the distribution of SLSs in ~~40 wholly-sequenced bacterial genomes~~ and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.	+	We performed a first systematic analysis of the distribution of SLSs in and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.

	A second analysis based on clustering procedures revealed that 29 out of 40 analyzed genomes have SLSs that can be grouped by sequence similarities. Such SLSs corresponding to about 1% of the whole population and have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Further refinements led to identify 92 families of repeated sequence, mostly sharing a common SLS. 25 of them include all well-known SLS containing repeats and some families reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions.		A second analysis based on clustering procedures revealed that 29 out of 40 analyzed genomes have SLSs that can be grouped by sequence similarities. Such SLSs corresponding to about 1% of the whole population and have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Further refinements led to identify 92 families of repeated sequence, mostly sharing a common SLS. 25 of them include all well-known SLS containing repeats and some families reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions.

Luca at 16:02, 20 June 2007

Luca — Wed, 20 Jun 2007 16:02:06 GMT

←Older revision		Revision as of 16:02, 20 June 2007
Line 1:		Line 1:
-	Bacterial genomes are generally compact and most of their sequence is involved in protein coding, but a growing number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. Many of these sequences are active as RNA and often contain simple stem-loop structures (SLS), essential to their functionality ~~and in some cases they are described as repeated and very abundant component of bacterial genome~~. ~~For this reason a systematic analysis of the distribution of appeared of interest~~	+	[[Image:Bacterial_pae.jpg\|300px\|right\|thumb\|PAE-1 bacterial family secondary structure]]
-	~~Our research focused on the identification~~ of sequences ~~able to fold~~ in a ~~stem loop structure (SLS)~~	+	Bacterial genomes are generally compact and most of their sequence is involved in protein coding, but a growing number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. Many of these sequences are active as RNA and often contain simple stem-loop structures (SLS), essential to their functionality. Moreover, families of repeated sequences, sharing a common SLS, have been described in many bacterial genomes even if only in few cases a clear biological function was assessed. In order to quantify this phenomenon we performed a systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes which are representative of the whole bacterial world. In this way we demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition.
-		+	a large collection of families of repeated stem-loop containing sequences has been identified by clustering stemloop structures according to sequence similarity in the analyzed species. Secondary structure analysis reveals the presence of a large number of sequences where a conserved secondary structure may be demonstrated within the family.
-		+
-	to ~~identify~~ systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition.	+
-		+
-	A large collection of families of repeated stem-loop containing sequences has been identified by clustering stemloop structures according to sequence similarity in ~~40 bacterial~~ species~~, representative of the whole bacterial world~~. Secondary structure analysis reveals the presence of a large number of sequences where a conserved secondary structure may be demonstrated within the family.	+

	We performed a first systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.		We performed a first systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.

Giovanni at 15:24, 20 June 2007

Giovanni — Wed, 20 Jun 2007 15:24:15 GMT

←Older revision		Revision as of 15:24, 20 June 2007
Line 14:		Line 14:
	* [http://www.biomedcentral.com/1471-2164/7/170 PETRILLO M., SILVESTRO G., DI NOCERA PP., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170]		* [http://www.biomedcentral.com/1471-2164/7/170 PETRILLO M., SILVESTRO G., DI NOCERA PP., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170]
	* COZZUTO L., PETRILLO M., SILVESTRO G., DI NOCERA PP. and PAOLELLA G. Systematic identification of stem-loop containing sequence families in bacterial genomes SUBMITTED.		* COZZUTO L., PETRILLO M., SILVESTRO G., DI NOCERA PP. and PAOLELLA G. Systematic identification of stem-loop containing sequence families in bacterial genomes SUBMITTED.
		+
		+
		+	{{footer reslines}}

Luca at 15:18, 19 June 2007

Luca — Tue, 19 Jun 2007 15:18:22 GMT

←Older revision		Revision as of 15:18, 19 June 2007
Line 1:		Line 1:
-	~~Most of bacterial~~ genomes is involved in protein coding, but a number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression ~~both at DNA and RNA level~~.	+	Bacterial genomes are generally compact and most of their sequence is involved in protein coding, but a growing number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. Many of these sequences are active as RNA and often contain simple stem-loop structures (SLS), essential to their functionality and in some cases they are described as repeated and very abundant component of bacterial genome. For this reason a systematic analysis of the distribution of appeared of interest
-	~~These~~ sequences often are able to fold as a stem-loop ~~based structures~~ (SLS) and ~~this feature is indispensable~~ to ~~their biological functions~~.	+	Our research focused on the identification of sequences able to fold in a stem loop structure (SLS)
		+
		+
		+	to identify systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition.
		+
		+	A large collection of families of repeated stem-loop containing sequences has been identified by clustering stemloop structures according to sequence similarity in 40 bacterial species, representative of the whole bacterial world. Secondary structure analysis reveals the presence of a large number of sequences where a conserved secondary structure may be demonstrated within the family.

	We performed a first systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.		We performed a first systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.

Luca at 15:14, 18 June 2007

Luca — Mon, 18 Jun 2007 15:14:22 GMT

←Older revision		Revision as of 15:14, 18 June 2007
Line 1:		Line 1:
	Most of bacterial genomes is involved in protein coding, but a number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression both at DNA and RNA level.		Most of bacterial genomes is involved in protein coding, but a number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression both at DNA and RNA level.
	These sequences often are able to fold as a stem-loop based structures (SLS) and this feature is indispensable to their biological functions.		These sequences often are able to fold as a stem-loop based structures (SLS) and this feature is indispensable to their biological functions.
		+
	We performed a first systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.		We performed a first systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.
		+
	A second analysis based on clustering procedures revealed that 29 out of 40 analyzed genomes have SLSs that can be grouped by sequence similarities. Such SLSs corresponding to about 1% of the whole population and have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Further refinements led to identify 92 families of repeated sequence, mostly sharing a common SLS. 25 of them include all well-known SLS containing repeats and some families reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions.		A second analysis based on clustering procedures revealed that 29 out of 40 analyzed genomes have SLSs that can be grouped by sequence similarities. Such SLSs corresponding to about 1% of the whole population and have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Further refinements led to identify 92 families of repeated sequence, mostly sharing a common SLS. 25 of them include all well-known SLS containing repeats and some families reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions.

Luca at 15:12, 18 June 2007

Luca — Mon, 18 Jun 2007 15:12:42 GMT

←Older revision		Revision as of 15:12, 18 June 2007
Line 2:		Line 2:
	These sequences often are able to fold as a stem-loop based structures (SLS) and this feature is indispensable to their biological functions.		These sequences often are able to fold as a stem-loop based structures (SLS) and this feature is indispensable to their biological functions.
	We performed a first systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.		We performed a first systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.
-	A second analysis revealed that 29 out of 40 analyzed genomes have ~~a number of~~ SLSs ~~which~~ can be grouped by sequence similarities. Such SLSs corresponding to about 1% of the whole population and have a substantially higher aptitude to fold into a stable secondary structure than the initial set.	+	A second analysis based on clustering procedures revealed that 29 out of 40 analyzed genomes have SLSs that can be grouped by sequence similarities. Such SLSs corresponding to about 1% of the whole population and have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Further refinements led to identify 92 families of repeated sequence, mostly sharing a common SLS. 25 of them include all well-known SLS containing repeats and some families reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions.
-		+
-	~~SLSs selected in this way Regrouping~~ of ~~the selected sequences by~~ sequence ~~similarity~~, ~~strand reciprocity and genomic location allowed to remove redundancies. HMM analysis was used to define~~ a ~~final set of 92 families~~. 25 of them include all well-known SLS containing repeats and some families reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions.	+
-		+
-	~~Conclusions~~	+
-	Systematic analysis of 40 bacterial genomes revealed a large number of repeated sequence families, including known and novel ones. Their predicted structure and genomic location suggest that even in compact bacterial genomes, a relatively large fraction of the genome consists of non-protein-coding sequences, possibly functioning at RNA level.	+
-		+
-		+

	== References ==		== References ==
	* [http://www.biomedcentral.com/1471-2164/7/170 PETRILLO M., SILVESTRO G., DI NOCERA PP., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170]		* [http://www.biomedcentral.com/1471-2164/7/170 PETRILLO M., SILVESTRO G., DI NOCERA PP., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170]
	* COZZUTO L., PETRILLO M., SILVESTRO G., DI NOCERA PP. and PAOLELLA G. Systematic identification of stem-loop containing sequence families in bacterial genomes SUBMITTED.		* COZZUTO L., PETRILLO M., SILVESTRO G., DI NOCERA PP. and PAOLELLA G. Systematic identification of stem-loop containing sequence families in bacterial genomes SUBMITTED.

Luca at 11:45, 18 June 2007

Luca — Mon, 18 Jun 2007 11:45:35 GMT

←Older revision		Revision as of 11:45, 18 June 2007
Line 1:		Line 1:
-	~~Bacterial~~ genomes ~~are generally compact and most of their sequence~~ is involved in protein coding, but a ~~growing~~ number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. ~~Many of these~~ sequences are ~~active~~ as ~~RNA and often contain simple~~ stem-loop structures~~, essential~~ to their ~~functionality~~. ~~A large collection~~ of ~~families~~ of ~~repeated stem~~-~~loop containing~~ sequences ~~has been identified~~ by ~~clustering stemloop structures according~~ to sequence similarity in ~~40 bacterial species~~, ~~representative~~ of the ~~whole bacterial world. Secondary~~ structure analysis ~~reveals the presence~~ of a large number of ~~sequences where a conserved secondary~~ structure ~~may be demonstrated within~~ the ~~family~~.	+	Most of bacterial genomes is involved in protein coding, but a number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression both at DNA and RNA level.
		+	These sequences often are able to fold as a stem-loop based structures (SLS) and this feature is indispensable to their biological functions.
		+	We performed a first systematic analysis of the distribution of SLSs in 40 wholly-sequenced bacterial genomes and demonstrated that SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and base composition. We also detect an enrichment of specific, non random, SLS sub-populations of higher stability within the intergenic regions of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all evaluated species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs.
		+	A second analysis revealed that 29 out of 40 analyzed genomes have a number of SLSs which can be grouped by sequence similarities. Such SLSs corresponding to about 1% of the whole population and have a substantially higher aptitude to fold into a stable secondary structure than the initial set.
		+
		+	SLSs selected in this way Regrouping of the selected sequences by sequence similarity, strand reciprocity and genomic location allowed to remove redundancies. HMM analysis was used to define a final set of 92 families. 25 of them include all well-known SLS containing repeats and some families reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions.
		+
		+	Conclusions
		+	Systematic analysis of 40 bacterial genomes revealed a large number of repeated sequence families, including known and novel ones. Their predicted structure and genomic location suggest that even in compact bacterial genomes, a relatively large fraction of the genome consists of non-protein-coding sequences, possibly functioning at RNA level.
		+
		+

	== References ==		== References ==
-	* [http://www.biomedcentral.com/1471-2164/7/170 PETRILLO M., SILVESTRO G., DI NOCERA P., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170]	+	* [http://www.biomedcentral.com/1471-2164/7/170 PETRILLO M., SILVESTRO G., DI NOCERA PP., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170]
		+	* COZZUTO L., PETRILLO M., SILVESTRO G., DI NOCERA PP. and PAOLELLA G. Systematic identification of stem-loop containing sequence families in bacterial genomes SUBMITTED.

Luca at 16:00, 12 June 2007

Luca — Tue, 12 Jun 2007 16:00:42 GMT

←Older revision		Revision as of 16:00, 12 June 2007
Line 1:		Line 1:
	Bacterial genomes are generally compact and most of their sequence is involved in protein coding, but a growing number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. Many of these sequences are active as RNA and often contain simple stem-loop structures, essential to their functionality. A large collection of families of repeated stem-loop containing sequences has been identified by clustering stemloop structures according to sequence similarity in 40 bacterial species, representative of the whole bacterial world. Secondary structure analysis reveals the presence of a large number of sequences where a conserved secondary structure may be demonstrated within the family.		Bacterial genomes are generally compact and most of their sequence is involved in protein coding, but a growing number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. Many of these sequences are active as RNA and often contain simple stem-loop structures, essential to their functionality. A large collection of families of repeated stem-loop containing sequences has been identified by clustering stemloop structures according to sequence similarity in 40 bacterial species, representative of the whole bacterial world. Secondary structure analysis reveals the presence of a large number of sequences where a conserved secondary structure may be demonstrated within the family.
		+
		+	== References ==
		+	* [http://www.biomedcentral.com/1471-2164/7/170 PETRILLO M., SILVESTRO G., DI NOCERA P., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170]