Box C/D snoRNAs

The table below gives an overview of box C/D snoRNAs in Cryptococcus and related Tremellomycetes. The ncRNAs were identified by phylogenetic comparison based on experimental data: siRNA libraries for H99 [Dumesic-2013, Burke-2019], JEC21 [GSE178393] and RNA-Seq libraries [Wallace-2020]. Sequence coordinates were from [Wallace-2020] [2]. The identified snoRNAs and their predicted modification targets would need experimental confirmation by deletion analysis and mapping (using RNaseH or reverse transcription assays) while co-purification with box CD snoRNP proteins, say combined with cross-linking [van.Nues-2011], could test whether the list has been exhaustive.

Nomenclature of Cryptococcal snoRNAs proposed here, is based on the following guide-lines:

• If the snoRNA is predicted to modify the same position as a known orthologue in yeast (primary) or another organism, use the name of the primary orthologue (to ease cross-comparison).

• If both yeast and human orthologues are found, combine both names with a dash.

• If D’ - and D-guide have different orthologues combine names of primary orthologues with underscores (omit other orthologue names).

• If no orthologues are found, name the snoRNA after the gene it originates from (ncRNA-gene annotations are available for C. neoformans H99).

• For duplicate snoRNAs with the same structure or target for a guide, use the same name; extend with b for one of the two copies.

• For snoRNAs with similar roles (as expected because of known orthologues) but different guides, use the same name but extend with -II for the second copy.

Genome coordinates in the tables below refer to C. deneoformans JEC21 the author worked with and are also in jec21-ncRNA.gtf. Coordinates for snoRNAs of C. neoformans H99 are in h99-ncRNAxtra.gtf.

As indicated on individual snoRNA pages, for some snoRNAs the base pairing of the guide to a target site is not perfect (mismatches or skipped nucleotides are surrounded by square brackets). When available, accessory guide sequences [van.Nues-2011] have been indicated; their target sequence is in between round brackets, extending the sequence recognized by the guide linked to a D/D’ motif. Question marks indicate that support for a modification is solely based on complimentarity to a putative guide sequence (plus phylogenetic evidence for snoRNAs or target sites), but without experimental data as available for orthologous modifications in other organisms. Hints for putative secondary structures are predominantly for snoRNAs of Tremellomycetes and helped to identify putative (irregular) D’ and C’ motifs which are often brought together by a helix [van.Nues-2011]. In Annot annotation lines, canonical motifs for C/C’ (rugauga) and D/D’ (cuga) boxes indicate the regions that might function as such; preceding the D/D’ boxes and above conserved (accessory) guide sections the reverse target RNA sequences are indicated (with U instead of T) [1]

Tables

Chromosomes

1 & 2

No.	Location [3]	Name [4]	Guide @	Target	JEC21 [5]	H99 [5]	Description	Host gene name
Chromosome 1
1.1	1:347703:347820:-1	snR66	D’	25S		CNAG_12022	snR66_processed-boxCDsnoRNA-118nt-as-URS000035E911_235443
1.2	1:727141:727245:1	SNORD16	D’		intron-CNA02800	intron-CNAG_00292	SNORD16_intronic-boxCDsnoRNA-87nt-in-CNA02800
1.3	1:1087293-1087392:-1	snR38	D’	18S	intron-CNA04050	intron-CNAG_00417	snR38_intronic-boxCDsnoRNA-91nt-in-CNA04050	Elongation factor 1-gamma EF1G
1.4	1:1178004-1178087:1 + 1:1178140-1178151:1 XM_024656271.1:123-222	snR50 snR40l	D’ D	25S, ETS1? 25S	intron-CNA04380	intron-CNAG_00458	snR50_snR40l_intronic-boxCDsnoRNA-101nt-in-CNA04380	transcriptional regulatory protein RXT2
1.5	1:1178296-1178387:1	snR74	D’	18S	intron-CNA04380	intron-CNAG_00458	snR74_intronic-boxCDsnoRNA-92nt-in-CNA04380	transcriptional regulatory protein RXT2
1.6	1:1727324:1727412:1	snR39b	D	25S	intron-CNA06360	intron-CNAG_00656	snR39b_intronic-boxCDsnoRNA-87nt-in-CNA06360	large subunit ribosomal protein L7e
1.7	1:1859589:1859671:1	snRcnag12093	D’	?	intron	intron-CNAG_12093	snRcnag12093_intronic-boxCDsnoRNA-83nt
1.8	1:2196292:2196381:-1	snR60-Z15	D’	25S	intron-CNA07960	intron-CNAG_00819	snR60-Z15_intronic-boxCDsnoRNA-in-S30-CNA07960-90nt	40S ribosomal protein S30
			D	25S
Chromosome 2
2.1	2:323413:323506:-1	snR73-snoZ3 as 12.4	D’	25S	intron-CNB01050	intron-CNAG_03602	snR73-snoZ3_intronic-boxCDsnoRNA-93nt-in-Utp12-CNB01050	UTP12
2.2	2:323677:323796:-1	snR77	D’	18S	intron-CNB01050	intron-CNAG_03602	snR77_intronic-boxCDsnoRNA-118nt-in-UTP12-CNB01050	UTP12
2.3	2:323954:324038:-1	snR78	D’	25S	intron-CNB01050	intron-CNAG_03602	snR78_intronic-boxCDsnoRNA-84nt-in-UTP12-CNB01050	UTP12
2.4	2:436587:436684:1	SNORD96	D	5.8S	intron-CNB01450	intron-CNAG_03645	SNORD96_intronic-boxCDsnoRNA-97nt-in-UTP17-CNB01450	UTP17
2.5	2:436830:436916:1	SnoR29 as 2.9	D’	25S	intron-CNB01450	intron-CNAG_03645	SnoR29_intronic-boxCDsnoRNA-86nt-in-UTP17-CNB01450	UTP17
2.6	2:661388:661496:-1	SNORD110	D’	18S	intron-CNB02280	intron-CNAG_03730	SNORD110_intronic-boxCDsnoRNA-109nt-in-CNB02280	DNA-directed-RNA-polymerase-II-subunit RPB11
2.7	2:770753:770855:-1	SNORD49	D’	25S	intron	intron-CNAG_12167	SNORD49_intronic-boxCDsnoRNA-102nt-in-transcript-as-CNAG_12167
2.8	2:976734:977264:1	SCARNA6	D’	U5	intron-CNB03235	intron-CNAG_03835	SCARNA6_intronic-boxCDsnoRNA-535nt-in-CNB03235	DASH-complex-subunit DAD3
2.9	2:1309856-1309773:-1	snoZ107-SnoR29b as 2.5	D’	25S	intron-CNB04560	intron-CNAG_03967	snoZ107-SnoR29b_intronic-boxCDsnoRNA-84nt-in-CNB04560	F-actin capping protein

3 & 4

No.	Location	Name	Guide @	Target	JEC21	H99	Description	Host gene name
Chromosome 3
3.1	3:34179:34306:1	snR48-SNORD60	D’	25S	intron	intron-CNAG_12216	snR48-SNORD60_intronic-boxCDsnoRNA-127nt-as-CNAG_12216
3.2	3:133192-133288:-1	snR40 snR56-SNORD25	D’ D	18S 18S	intron-CNC00470	intron-CNAG_03038	snR40_snR56_intronic-boxCDsnoRNA-96nt-in-CNC00470
3.3	3:133588:133674:-1	SNORD79	D’	25S	intron-CNC00470	intron-CNAG_03038	SNORD79_intronic-boxCDsnoRNA-83nt-in-CNC00470
3.4	3:516393:516472:1	snR51s-SNORD57	D’	18S	intron-CNC01900	intron-CNAG_01679	snR51s-SNORD57_intronic-boxCDsnoRNA-79nt-in-CNC01900	small subunit ribosomal protein S15
3.5	3:1081077:1081184:1	U18-SNORD18	D’	25S	intron-CNC03420	intron-CNAG_02714	U18-SNORD18_intronic-boxCDsnoRNA-in-CNC03420	elongation factor 1-beta_EF1-beta
3.6	3:1117283:1117380:-1	snR40-like	D’	18S	intron	intron-CNAG_12274	snR40-like_intronic-boxCDsnoRNA-97nt
3.7	3:1181929:1182027:1	SnoR30	D’	18S	intron-CNC03760	intron-CNAG_02754	SnoR30_intronic-boxCDsnoRNA-98nt-in-CNC03760	small subunit ribosomal protein S12
3.8	3:1289251:1289367:-1	snR47-SNORD36C	D’	25S	processed	CNAG_12265	snR47-SNORD36C_processed-boxCDsnoRNA-116nt-as-CNAG_12265	on transcript with RNAse MRP
3.9	3:1393759:1393922:1	snR63-SNORD46	D	25S	intron	intron-CNAG_12258	snR63-SNORD46_intronic-boxCDsnoRNA-163nt-as-CNAG_12258
3.10	3:1423203:1423300:-1	snR13	D’	25S	intron	intron-CNAG_12256	snR13_intronic-boxCDsnoRNA-as-CNAG_12256
3.11	3:1423432:1423685:-1	snR45-U13/U3a as 8.6		18S	exon	exon-CNAG_12256	snR45-U13_U3a_exonic-boxCDsnoRNA-253nt-as-CNAG_12256
3.12	3:1459140:1459254:1	snR67-snoU31b	D’	25S	intron-CNC04820	intron-CNAG_02867	snR67-snoU31b_intronic-boxCDsnoRNA-115nt-in-CNC04820	Phosphoinositide phospholipase C (PLC1)
3.13	3:1459486:1459570:1	snR53	D’	18S	intron-CNC04820	intron-CNAG_02867	snR53_intronic-boxCDsnoRNA-84nt-in-CNC04820	Phosphoinositide phospholipase C (PLC1)
3.14	3:1489804:1489899:-1	snR69	D’	25S	intron-CNC04930	intron-CNAG_02880	snR69_intronic-boxCDsnoRNA-95nt-in-CNC04930	Obg-like ATPase 1
Chromosome 4
4.1	4:194959:195105:1	snR190-SNORD12B	D’	25S	intron-CND00700	intron-CNAG_00930	snR190_intronic-boxCDsnoRNA-145nt-in-5UTR-CND00700	Argininosuccinate synthase
4.2	4:195235:195504:1	U14-SNORD14A		18S	intron-CND00700	intron-CNAG_00930	U14_intronic-boxCDsnoRNA-258nt-in-5UTR-CND00700	Argininosuccinate-synthase
4.3	4:303065:303213:1 4:303380:303484:1	snoU2-30_25S snoU2-30	D’ ? D	25S? U2	intron	intron-CNAG_12489	snoU2-30_intronic-boxCDsnoRNA-141nt-in-transcript-with-3-boxCDsnoRNAs-1098nt
4.4	4:303380:303484:1 4:303380:303484:1	snR41_25S snR41	D’ ? D	25S? 18S	intron	intron-CNAG_12489	snR41_intronic-boxCDsnoRNA-104nt-in-transcript-with-3-boxCDsnoRNAs-1098nt
4.5	4:303634:303759:1	snR70	D’	18S	intron	intron-CNAG_12489	snR70_intronic-boxCDsnoRNA-125nt-in-transcript-with-3-boxCDsnoRNAs-1098nt
4.6	4:416341:416495:1	snR45-II		18S	processed	CNAG_12486	snR45-II_processed-boxCDsnoRNA-154nt-as-CNAG_12486
4.7	4:1267488:1267654:-1	snRcnag12441	D D	18S?, 25S? U1?	intron	intron-CNAG_12441	snRcnag12441_intronic-boxCDsnoRNA-151nt-in-transcript-as-CNAG_12441
4.8	4:1303746:1303850:-1	snR64-SNORD74	D’	25S	intron-CND04750	intron-CNAG_01359	snR64-SNORD74_intronic-boxCDsnoRNA-105nt-in-CND04750	DNA-directed RNA polymerase II subunit RPB7

5 - 9

No.	Location	Name	Guide @	Target	JEC21	H99	Description	Host gene name
Chromosome 5
5.1	5:865875:866011:1	snRcne03050 SNORD30	D’ D ?	25S ?	intron-CNE03050	intron-CNAG_02236	snRcne03050_SNORD30_intronic-boxCDsnoRNA-in-CNE03050	Serine/threonine-protein phosphatase
5.2	5:994451:994532:1	snR62	D’	25S	intron-CNE03520	intron-CNAG_02185	snR62_intronic-boxCDsnoRNA-81nt-in-CNE03520	RCM1 LSU (Cytosine-C(5))-Methyltransferase
Chromosome 6
6.1	6:285915:285991:1	snR71-SNORD29 as 14.1	D’	25S	intron-CNF00890	intron-CNAG_05884	snR71_intronic-boxCDsnoRNA-76nt-in-CNF00890	Importin beta-4 subunit
6.2	6:436487:436607:1	snR72	D’	25S	intron-CNF00890	intron-CNAG_05884	snR72_intronic_boxCDsnoRNA-122nt-in-CNF01490-as-CNAG_12684	exonic HACAsnoRNA; integrase-like protein
6.3	6:436487:436607:1	snRcnf04440	D’	18S?	5UTR-CNF00890	intron-CNAG_05884	snRcnf04400_boxCDsnoRNA-in-CNF04440	proteins involved in DNA maintenance ?
Chromosome 7
7.1	7:71277-71361:1	snRcng00300	D’	25S?	intron-CNF00890	intron-CNAG_05884	snRcng00300_intronic-boxCDsnoRNA-85nt-in-CNG0300	60S acidic ribosomal protein P0
7.2	7:797684:797771:-1	snR58	D’	25S	intron-CNG02860	intron-CNAG_03289	snR58_intronic-boxCDsnoRNA-87nt-in-CNG02860	Methionine aminopeptidase 2
7.3	7:1026933:1027023:-1	snR41 SNORD7	D’ D	18S (x2) U6	intron-CNG03660	intron-CNAG_03203	snR41-SNORD7_intronic-boxCDsnoRNA-90nt-in-CNG03660	DNA polymerase epsilon p12 subunit
Chromosome 8
8.1	8:118872:118970:1	snR52-SNORD83	D	18S	intron-CNH03660	intron-CNAG_05285	snR52-SNORD83_intronic-boxCDsnoRNA-98nt-in-CNH03440	SCD6/LSM13
8.2	8:303969:304059:-1	snR51-SNORD41 snR79	D’ D	25S 18S	intron	intron-CNAG_05651	snR51_snR79_intronic-boxCDsnoRNA-90nt	non-coding transcript with two exons, each containing an HACA snoRNA
8.3	8:681932:682016:1	snR88	D’ D	18S (25S?) 25S (x2)	intron-CNH01600	intron-CNAG_07884	snR88_intronic-boxCDsnoRNA-84nt-in-CNH01600	37S ribosomal protein S35, mitochondrial
8.4	8:682138:682266:1	snRcnh01600	D’	25S	intron-CNH01600	intron-CNAG_07884	snRcnh01600_intronic-boxCDsnoRNA-70nt-in-CNH01600	37S ribosomal protein S35, mitochondrial
8.5	8:822140:822224:1	U24-SNORD24	D’ D	25S (x2) 25S	intron-CNH01270	intron-CNAG_05465	U24_intronic-boxCDsnoRNA-88nt-in-CNH01270	Guanine nucleotide-binding protein subunit beta-like protein (Ribosomal protein RACK1 subfamily)
8.6	8:892818-893068:1	U3b as 3.11		18S		CNAG_13174	U3b_boxCDsnoRNA-251nt-as-CNAG_13174
Chromosome 9
9.1	9:960594:960686:1	snR67d	D	25S	intron	intron-CNAG_12831	snR67d_intronic-boxCDsnoRNA-92nt-as-CNAG_12831

10 - 14

No.	Location	Name	Guide @	Target	JEC21	H99	Description	Host gene name
Chromosome 10
Chromosome 11
11.1	11:703167:703251:-1	snRcnk02420-2	D	18S	intron-CNK02420	intron-CNAG_13018	snRcnk02420-2_intronic-boxCDsnoRNA-82nt-in-CNK02420pseu-as-CNAG_13018
11.2	11:703406:703495:-1	snRcnk02420-1	D’ D	18S 25S	intron-CNK02420	intron-CNAG_13018	snRcnk02420-1_intronic-boxCDsnoRNA-82nt-in-CNK02420pseu-as-CNAG_13018
Chromosome 12
12.1	12:98982:99100:-1	snR76-SNORD88	D’	25S	intron-CNL04010	intron-CNAG_05228	snR76_intronic-boxCDsnoRNA-118nt-in-CNL04010	U3 small nucleolar ribonucleoprotein LCP5
12.2	12:388390-388472:1	snR61-SNORD38	D’	25S	intron-CNL04930	intron-CNAG_07813	snR61_intronic-boxCDsnoRNA-83nt-in-CNL04930	Transcription initiation factor TFIID subunit 13
12.3	12:388603-388881:1	SNORD17	D’	25S	intron-CNL04930	intron-CNAG_07813	snR61_intronic-boxCDsnoRNA-83nt-in-CNL04930	Transcription initiation factor TFIID subunit 13
12.4	12:540590:540681:1	snR73b as 2.1	D’	25S	intron-CNL05500	intron-CNAG_05070	snR73b_intronic-boxCDsnoRNA-91nt-in-CNL05500	Sulfite reductase (NADPH) hemoprotein
Chromosome 13
13.1	13:508266-508382:1	snR55	D	18S	intron-CNM01680	intron-CNAG_06167	snR55_intronic-boxCDsnoRNA-117nt-in-CNM01680	Metal homeostatis protein bsd2
Chromosome 14
14.1	14:40441:40535:-1	snR71b as 6.1	D’ D ?	25S 25S?	intron	intron-CNAG_13104	snR71b_intronic-boxCDsnoRNA-96nt-as-CNAG_13104
14.2	14:229754:229973:1	snR75-SNORD15	D’	25S	intron-CNN00700	intron-CNAG_06340	snR75-SNORD15_intronic-boxCDsnoRNA-220nt-in-CNN00700	Pre-rRNA-processing protein TSR4

---

The snoRNAs were identified as follows, basically as done before for [van.Nues-2011] and [Sharma-2017]:

• Collect sequence for peaks in unspecific data that derived from non-coding sequences (i.e. not properly annotated).

• Check Rfam and RNAcentral.

• Select homologues from output of NCBI-blast with snoRNA sequence.

• Align manually (the D/C and C’/D’ boxes will form structural units not detected by aligners) in Jalview and use conserved bits to check:

  • supplementary data from [van.Nues-2011] for yeast orthologues/homologues.

  • the snoRNA Orthological Gene Database snOPY [Yoshihama-2013] for other orthologues/homologues.

  • whether guide fits D/D’ box and conserved regions.

• For snoRNAs derived from transcripts where only the introns contain conserved regions:

  • locate splice sites (5’SS:GTRrGT, 3’SS: YAG) and branch point (BP: CTGA) [Janbon-2014] to test alignment.

• Check whether secondary structure (i.e. stem-loop) bring D’ (CTGA) and C’ (RTGATGA) boxes together, helping to identify irregular ones [van.Nues-2011].

  • Annotate alignments and save in Stockholm format.

  • Export image.

  • Draw secondary structure with R2R (for some snoRNAs, for example U3b).

  • Edit figure in Inkscape.

• IGB genome browser images of the expressed ncRNA use traces from H99 [Burke-2019, Wallace-2020].

Notes

[1]

In [van.Nues-2011] we used inverse contrast and colour to indicate target RNA sequences and marked the motifs with their names; fasta/stockholm formatting does not allow for this.

[2]

The reference files were obtained as described in the script wget_resources.sh that comes with the source code (in coalispr/resources/share/bash_scripts/).

[3]

The provided genomic coordinates were used for searching homologs and might contain flanking sequences. Coordinates fitting the 5’ and 3’ ends of RNA-Seq traces are given with the sequence on the snoRNA page.

[4]

Names of box C/D snoRNAs refer to orthologs initially found for human (SNOR), baker’s yeast (snR) or plant (Arabidopsis thalia, Oryza sativa and Aegilops_tauschii) and are retrievable from individual snoRNA pages through links to the snoRNA Orthological Gene Database   snOPY.

[5] (1,2)

These columns describe the genomic context of the snoRNA.