Ribosome

The ribosome in FANTOM 5

Components

Kegg pathway: http://www.genome.jp/kegg/pathway/ko/ko03010.html

S20, L3, L4, L24A, L8, S15, L17, S3, L10 and L35 are presented in the same line, but I do not understand why.  Nevertheless, I started with these subunit proteins. --Plessy 08:18, 9 August 2011 (UTC)

rRNA

28S / LSUrRNA http://www.genome.jp/dbget-bin/www_bget?K01982 5S / LSU5S http://www.genome.jp/dbget-bin/www_bget?K01981 5.8S / LSU5.8S http://www.genome.jp/dbget-bin/www_bget?K01986 18S / SSUrRNA / http://www.genome.jp/dbget-bin/www_bget?K01979

See also rDNA page.

Proteins

Small sub-unit

RPS20-0		chr8:56987051..56987072,-	~70 nt downstream the RefSeq 5′ end.  Upstream antisense TSS follow RefSeq, not CAGE and Entrez gene.
RPS15-0		chr19:1438351..1438409,+	No snoRNA. Not much exon painting in CAGEscan either.
RPS3-0		chr11:75110552..75110578,+
RPS11-0		chr19:49999681..49999705,+
RPS4Y1-0	chrY:2709631..2709653,+		No snoRNA. See also RPS4Y2 and RPS4X1.
RPS4Y2-0	chrY:22918021..22918034,+	No snoRNA. See also RPS4Y1 and RPS4X1. Not detected in CAGEscan, low in hCAGE.
RPS4Y2-1	chrY:22917988..22918000,+	No snoRNA. See also RPS4Y1 and RPS4X1. Not detected in CAGEscan, low in hCAGE.
RPS4X1+1	chrX:71497062..71497073,-	This is the major TSS in CAGEscan.
RPS4X1-0	chrX:71497085..71497107,-
RPS4X1-1	chrX:71497113..71497120,-
RPS29-0		chr14:50053081..50053108,-	Much less exon painting than usual in CAGEscan (exons difficult to map in hCAGE). Same observation with mouse CAGEscan.  Neighbour of a 7SL copy in human and mouse.
RPS2-0		chr16:2014810..2014835,-	Promoter almost undetectable with CAGEscan.
RPS18-0		chr6:33239844..33239859,+	No snoRNA.  Sharper promoter than usual.  Low exon mapability in hCAGE and not much painting in CAGEscan.
RPS14-1		chr5:149829314..149829325,-
RPS14-0		chr5:149829294..149829310,-	No snoRNA.  First exon difficult to map and second exon weakly painted in hCAGE.  First exon painted stronger then second exon, and intronic signal in CAGEscan.
RPS14+1		chr5:149829263..149829276,-
RPS14+2		chr5:149829239..149829255,-
RPS9-0		chr19:54704718..54704734,+	No snoRNA.  Exons partially unmappable in hCAGE, and clear but not too strong exon painting in CAGEscan.
RPS16-0		chr19:39926576..39926594,-	No snoRNA. Exons mappable in hCAGE, strong exon painting in CAGEscan.
RPS5-0		chr19:58898627..58898649,+	No snoRNA. Exons mappable in hCAGE, moderate exon painting in CAGEscan.
RPS23-0		chr5:81574160..81574192,-	No snoRNA. Exons mappable in hCAGE, strong exon painting in CAGEscan.
RPSA-0		chr3:39448201..39448222,+	hCAGE and CAGEscan disagree with most ESTs.  In that case, the mapability problem may be on the EST side.
RPS13-0		chr11:17099202..17099230,-	Exons quite mappable in hCAGE, moderate exon painting in CAGEscan.

RPS17 is in a blind spot of the human genome assembly hg19: the HeliScopeCAGE reads, and more surprisingly the CAGEscan reads (longer as pairs), fail to align there.

Large sub-unit

RPL3-0		chr22:39715618..39715634,-
RPL3-8		chr22:39716323..39716346,-	Small ALU upstream promoter; not enough CAGEscan reads to know if it bridges with RPL3.
RPL23A-0	chr17:27046987..27047011,+
RPL23A+3	chr17:27047280..27047297,+	Second most expressed after RPL23A-0
RPL8-0		chr8:146017765..146017814,-	Does not contain snoRNAs
RPL17-0		chr18:47018784..47018858,-	Strong discrepancy between hCAGE and CAGEscan for promoter shape.
RPL17-1		chr18:47018869..47018896,-
RPL17-2		chr18:47018897..47018922,-
RPL10-0		chrX:153626710..153626730,+	Not all exons mappable with hCAGE.  Some exon painting in CAGEscan.
RPL10-1		chrX:153626659..153626692,+	Second most expressed near RPL10-0
RPL10-3		chrX:153626616..153626627,+	Third most expressed near RPL10-0
RPL35-0		chr9:127624220..127624250,-
RPL23-0		chr17:37009968..37009998,-
RPL26-0		chr17:8286499..8286518,-	Does not contain snoRNAs
RPL11-0		chr1:24018278..24018303,+	Does not contain snoRNAs
RPL11-1		chr1:24018269..24018274,+
RPL9-0		chr4:39460520..39460574,-	Does not contain snoRNAs
RPL9+1		chr4:39460496..39460513,-
RPL9+2		chr4:39460471..39460486,-
RPL9+3		chr4:39460225..39460236,-	Supported by mRNAs.
RPL32-0		chr3:12883026..12883086,-
RPL32+36	chr3:12880839..12880852,-	3′ end of exon 3.
RPL19-0		chr17:37356527..37356611,+	Does not contain snoRNAs
RPL19+2		chr17:37356826..37356841,+
RPL5-0		chr1:93297586..93297610,+
RPL5+1		chr1:93297622..93297635,+
RPL7-0		chr8:74205851..74205875,-	Does not contain snoRNAs.  Painting does not distinguish exons in CAGEscan.
RPL7-1		chr8:74205888..74205923,-
RPL7-12		chr8:74206382..74206407,-
RPL7-15		chr8:74206559..74206574,-
RPL7-17		chr8:74206660..74206684,-
RPL7-18		chr8:74206685..74206724,-
RPL7+1		chr8:74205825..74205844,-
RPL7+3		chr8:74205478..74205485,-	Intronic, not seen in CAGEscan
RPL7+4		chr8:74205395..74205413,-	Intronic, not seen in CAGEscan
RPL7+6		chr8:74205299..74205314,-	Intronic, not seen in CAGEscan
RPL27-0		chr17:41150407..41150470,+	Does not contain snoRNAs.  Exons mappable with hCAGE.  Clear exon painting in CAGEscan.
RPL34-0		chr4:109541723..109541738,+	Does not contain snoRNAs.
RPL34+1		chr4:109541740..109541761,+
RPL14-0		chr3:40498815..40498838,+	Does not contain snoRNAs.  Low exon mapability in hCAGE and low exon painting in CAGEscan.
RPL18-0		chr19:49122427..49122447,-	Does not contain snoRNAs.  Exons mappable with hCAGE.  Clear exon painting in CAGEscan.
RPL13A-0	chr19:49990853..49990871,+	Low exon mapability in hCAGE and low exon painting in CAGEscan.
RPL30-0		chr8:99057760..99057783,-	Exons mappable with hCAGE.  Moderate exon painting in CAGEscan.
RPL7A-0		chr9:136215054..136215084,+	Promoter barely detectable in CAGEscan.
RPLP1-0		chr15:69745152..69745170,+	Does not contain snoRNAs.  Exons mappable with hCAGE.low exon painting in CAGEscan.
RPLP2-0		chr11:809963..809971,+		Exons mappable with hCAGE.  Exon painting in CAGEscan.
RPLP0+2		chr12:120638636..120638680,-
RPLP0+1		chr12:120638691..120638700,-
RPLP0-0		chr12:120638905..120638916,-	Does not contain snoRNAs.  Exons mappable with hCAGE.  Strong exon painting in CAGEscan.
RPL10A-0	chr6:35436138..35436194,+	Does not contain snoRNAs.  Low exon mapability in hCAGE, some exon painting in CAGEscan.
RPL10A+1	chr6:35436198..35436226,+	
RPL12-1		chr9:130213707..130213718,-
RPL12-0		chr9:130213674..130213690,-	Disagreement between CAGEscan and hCAGE for the main promoter, most probably because of low-mappable area in the UTR.  Few exon painter in CAGEscan.  SNORA65 strong in both libraries.
RPL13-0		chr16:89627061..89627100,+	Partially mappable with hCAGE.  Strong exon painting in CAGEscan.
RPL15-0		chr3:23958612..23958630,+	Does not contain snoRNAs.  Low exon mapability in hCAGE, strong exon painting in CAGEscan.
RPL15+1		chr3:23958632..23958651,+	Expression level very similar to RPL15-0.  Contains the main TSS in CAGEscan.

Biosynthesis accessories

Kegg pathway http://www.genome.jp/kegg-bin/show_pathway?ko03008

gene name cluster host gene comment

SNORD54-0	chr8:56986452..56986464,-	RPS20
SNORD83B-0	chr22:39709904..39709926,-	RPL3
SNORD83A-0	chr22:39711301..39711312,-	RPL3
RNU86-0		chr22:39712891..39712902,-	RPL3	Not detected by CAGEscan.
RNU86+1		chr22:39712869..39712879,-	RPL3	Not detected by CAGEscan.
SNORD43-0	chr22:39715110..39715122,-	RPL3	Sharp peak (326 tags) but no cluster in maxcount10.
SNORD18C-0	chr15:66793646..66793657,-	RPL4
SNORD18B-0	chr15:66794406..66794433,-	RPL4
SNORD16-0	chr15:66795240..66795251,-	RPL4
SNORD18A-0	chr15:66795641..66795665,-	RPL4
SNORD42B-0	chr17:27047565..27047576,+	RPL23A
SNORD4A-0	chr17:27049601..27049646,+	RPL23A
SNORD42A-0	chr17:27050444..27050470,+	RPL23A
SNORD4B-0	chr17:27050698..27050709,+	RPL23A
SNORD58C-0	chr18:47015669..47015681,-	RPL17	Stronger in hCAGE than CAGEscan; synonym: U58 (fits better with the hCAGE cluster).
SNORD58A-0	chr18:47017708..47017723,-	RPL17
SNORD58B-0	chr18:47018075..47018116,-	RPL17
SNORD15A-0	chr11:75111429..75111455,+	RPS3
SNORD15B-0	chr11:75115459..75115474,+	RPS3
SNORA70-0	chrX:153628617..153628628,+	RPL10
SNORD35B-0	chr19:50000973..50000982,+	RPS11
SNORA21-0	chr17:37009241..37009251,-	RPL23	Low expression, almost painted.  Three downstream peaks found by paraclu but not DPI.
RN7SL1-0	chr14:50053284..50053300,+	RPS29	Neighbor of RPS29 in human and mouse.
SNORA7A-0	chr3:12881932..12881950,-	RPL32	May not serve as alternative promoter of RPL32, or very rarely.  Strong in CAGEscan.
SNORA66-0	chr1:93306250..93306289,+	RPL5
SNORA66+1	chr1:93306380..93306391,+	RPL5
SNORD21-0	chr1:93302841..93302855,+	RPL5
SNORA78-2	chr16:2015050..2015075,+	RPS2	Upstream of RPS2
SNORA64-0	chr16:2013098..2013113,-	RPS2
SNORA10-0	chr16:2012461..2012468,-	RPS2
SNORD68-0	chr16:89627831..89627845,+	RPL13
SNORD32A-0	chr19:49993215..49993231,+	RPL13A
SNORD33-0	chr19:49993867..49993881,+	RPL13A
SNORD34-0	chr19:49994158..49994172,+	RPL13A
SNORD35A-0	chr19:49994425..49994439,+	RPL13A
SNORA72-0	chr8:99054414..99054445,-	RPL30
SNORD24-0	chr9:136216248..136216258,+	RPL7A
SNORD36B-0	chr9:136216947..136216958,+	RPL7A
SNORD36A-0	chr9:136217307..136217320,+	RPL7A
SNORD36A-1	chr9:136217272..136217283,+	RPL7A
SNORD36C-0	chr9:136217698..136217709,+	RPL7A
SNORA52-0	chr11:811679..811693,+		RPLP2
SNORA65-0	chr9:130210906..130210920,-	RPL12
SNORA6-0	chr3:39449880..39449888,+	RPSA
SNORA62-0	chr3:39452541..39452554,+	RPSA
SNORA62+1	chr3:39452623..39452629,+	RPSA
SNORD14B-0	chr11:17097394..17097416,-	RPS13
SNORD14A-0	chr11:17096275..17096313,-	RPS13

Possibly related genes

HSPA8-0		chr11:122932835..122932852,-	SNORD14C, SNORD14D, SNORD14E
SNORD14C-0	chr11:122930121..122930134,-	HSPA8
SNORD14D-0	chr11:122929695..122929707,-	HSPA8
SNORD14E-0	chr11:122928861..122928872,-	HSPA8.  Confirmed by CAGEscan.
SNORD14E-1	chr11:122928925..122928939,-	HSPA8.  Not in CAGEscan.
C20orf199	chr20:47895171..47895189,+	SNORD12, SNORD12B, SNORD12C (no DPI cluster for that one).
SNORD12		chr20:47897221..47897232,+	C20orf199
SNORD12B	chr20:47896856..47896875,+	C20orf199
MRPL1-1		chr4:78783882..78783911,+
MRPL1-0		chr4:78783972..78784001,+
TAF10-0		chr11:93474645..93474668,-
SNORA40-0	chr11:93468396..93468408,-	TAF10.  Main CAGEscan peak outside the cluster.
SNORA18-0	chr11:93466752..93466772,-	TAF10.
SNORA18+1	chr11:93466719..93466749,-	TAF10.	Weak in CAGEscan.
SNORD5-0	chr11:93466455..93466468,-	TAF10.
SNORA8-0	chr11:93465656..93465674,-	TAF10.
SNORA8+1	chr11:93465630..93465655,-	TAF10.	Confirmed in CAGEscan.
SNORA1-0	chr11:93465292..93465303,-	TAF10.
SNORD6-0	chr11:93464715..93464741,	TAF10.	Also weak in CAGEscan.
SNORA25-0	chr11:93463807..93463814,-	TAF10.
SNORA32-0	chr11:93464257..93464273,-	TAF10.
KIAA1731	chr11:93394807..93394904,+
SCARNA9-0	chr11:93454673..93454692,+	KIAA1731.
SCARNA9+1	chr11:93454705..93454716,+	KIAA1731.
SCARNA9+7	chr11:93454961..93455005,+	KIAA1731.
SPIN1-0		chr9:91003271..91003386,+

Expression

The following command transforms the above eye-friendly tables into proper tab-delimited format, stripping the comments.

 sed -e 's|\t\t|\t|' -e 's|:|\t|' -e 's|\.\.|\t|' -e 's|,|\t|' | cut -f1-5

similarly, the following command produces intervals useful with tabix or genome browsers.

 sed -e 's|\t\t|\t|' -e 's|:|\t|' -e 's|\.\.|\t|' -e 's|,|\t|' | awk '{print $2":"$3"-"$4}'

It can be used to retreive the promoter expression levels from the expression table of DPI clusters.

 grep -E '^\w+-0' promoters.txt | sed -e 's|\t\t|\t|' -e 's|:|\t|' -e 's|\.\.|\t|' -e 's|,|\t|' | awk '{print $1"\t"$2":"$3"-"$4}' | while read name coords ; do echo; echo -ne "$name\t" ; tabix tc.max_counts5.tpm.osc.txt.gz $coords | cut -f2 ; done | grep -v '^$'

Conventions

Data sources

UPDATE_012 clusters UPDATE_012 clusters expression

Promoter names

gene names ± ordinal distance from the major TSS

Since +0 equals −0, by convention +0 is not used. Mnemonic: 0 reminds the O letter, like in origin.

Example promoter name: SNORD54-0, RPL4-1, RPL23A+3

Bibliography

• Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome. Zhaolei Zhang, Paul Harrison, and Mark Gerstein. Genome Res. 2002. 12:1466-1482 10.1101/gr.331902.
• The architecture of mammalian ribosomal protein promoters. Robert P Perry. BMC Evolutionary Biology 2005, 5:15 doi:10.1186/1471-2148-5-15
• Systematic Clustering of Transcription Start Site Landscapes. Xiaobei Zhao, Eivind Valen, Brian J. Parker, Albin Sandelin. PLoS ONE 6(8): e23409. doi:10.1371/journal.pone.0023409

Side notes

• Many exons of ribosomal proteins look like having a low mapability, as judged by the lack of typical background in the HeliScopeCAGE libraries.
• Some large intergenic regions look like having an even lower mapability as they are completely devoid of tagis in both HeliScopeCAGE and CAGEscan libraries.
• Ribosomomics poster presented at the Koyo meeting: Media:Koyo_poster_21-ribosomomics.pdf.
• E-mail discussions in [fantom5:00896][fantom5-wp5:00234].