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. Author manuscript; available in PMC: 2026 Jan 6.
Published in final edited form as: Mol Cell. 2025 Dec 18;85(24):4678–4697.e12. doi: 10.1016/j.molcel.2025.11.019

Key resources table

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Monocolonal anti-FLAG M2 antibody Sigma Aldrich Cat#F1804
RRID:AB_262044
anti-BrdU BD Biosciences Cat#BD347580
RRID:AB 400326
anti-ssDNA antibody DSHB Cat#autoanti-ssDNA
RRID:AB_10805144
Monocolonal anti-FLAG M2 – Peroxidase (HRP) Sigma Aldrich Cat#A8592-2MG; RRID:AB_439702
Bacterial and virus strains
HM-34 (MG1655 (crl−) hfq-FLAG) Melamed et al., 2016 1 N/A
AS-87 (MG1655 cI857:kan pE:GFP) Oppenheim et al.,2005 2 N/A
AS-39 (BW25113 lamB::kan) Baba et al., 2006 3 N/A
AS-78 (BW25113 recA::kan) Baba et al., 2006 3 N/A
RN-10 (DY330 dnaA-SPA) Butland et al., 2005 4 N/A
RN-9 (DY330 dnaN-SPA) Butland et al., 2005 4 N/A
AS-92 (DY330 recF-SPA) Butland et al., 2005 4 N/A
AS-35 (MG1655 (crl+) hfq::kan) Melamed et al., 2020 5 N/A
AS-146 (MG1655) Sutton et al., 2004 6 N/A
AS-147 (MG1655 dnaN159ts) Sutton et al., 2004 6 N/A
TY044 (MG1655 + pALA3047) Yao et al., 2021 7 N/A
AS-10 (MG1655 (crl−)) lab stock ML001
AS-15 (MG1655 (crl+)) lab stock ML002
AS-37 (MG1655 (crl−) hfq::kan) current work ML003
AS-36 (MG1655 (crl+) lambda lysogen WT) current work ML004
AS-65 (MG1655 (crl+) lambda lysogen preSΔseed) current work ML005
AS-64 (MG1655 (crl+) lambda lysogen ΔpreS) current work ML006
AS-88 (MG1655 CI857:kan) current work ML007
AS-96 (MG1655 (crl+) lamB::kan) current work ML008
AS-72 (MG1655 (crl+) lambda lysogen WT, lamB::kan) current work ML009
AS-73 (MG1655 (crl+) lambda lysogen preSΔseed, lamB::kan) current work ML010
AS-74 (MG1655 (crl+) lambda lysogen ΔpreS, lamB::kan) current work ML011
AS-93 (MG1655 (crl−) dnaA-SPA) current work ML012
AS-94 (MG1655 (crl−) dnaN-SPA) current work ML013
AS-95 (MG1655 (crl−) recF-SPA) current work ML014
AS-79 (MG1655 (crl+) recA::kan) current work ML015
AS-82 (MG1655 (crl+) lambda lysogen WT, recA::kan) current work ML016
AS-80 (MG1655 (crl+) lambda lysogen preSΔseed, recA::kan) current work ML017
AS-81 (MG1655 (crl+) lambda lysogen ΔpreS, recA::kan) current work ML018
AS-89 (MG1655 (crl+) lambda lysogen WT, hfq::kan) current work ML019
AS-90 (MG1655 (crl+) lambda lysogen preSΔseed, hfq::kan) current work ML020
AS-91 (MG1655 (crl+) lambda lysogen ΔpreS, hfq::kan) current work ML021
SMS-127 (MG1655 (crl+) rnb::kan) Melamed et al., 2020 5 ML022
SMS-128 (MG1655 (crl+) rnc::cat) Melamed et al., 2020 5 ML023
SMS-131 (BW25113 rnr::kan) Baba et al., 2006 3 ML024
SMS-132 (BW25113 pnp::kan) Baba et al., 2006 3 ML025
SMS-133 (MG1655 (crl+) rnc::cat) Melamed et al., 2020 5 ML026
AS-128 (MG1655(crl+) dnaN:SPA) current work ML027
AS-129 (MG1655(crl+) lambda lysogen wt, dnaN:SPA) current work ML028
AS-130 (MG1655(crl+) lambda lysogen preSΔseed, dnaN:SPA) current work ML029
SMP-153 (MG1655 (crl−) + pXG0) Urban et al., 2007 8 ML030
AS-5 (MG1655 (crl−) + pXG10-SF) Corcoran et al., 2012 9 ML031
AS-76 (MG1655 (crl−)+ pNM46) Walling et al., 2022 10 ML032
AS-24 (NEB5α + pCP20) Cherepanov et al., 1995 11 ML033
AS-83 (DH5α + pGEM-3) Promega Corporation ML034
AS-104 (NEB5α + pKD46) Datsenko et al., 2000 12 ML035
RN-1 (NEB5α + pXG10-SF-danAN) current work ML036
RN-14 (NEB5α + pXG10-SF-danAN M1) current work ML037
AS-97 (NEB5α + pXG10-SF-danAN M2) current work ML038
AS-127 (NEB5α + pXG10-SF-danAN M3) current work ML039
AS-158 (NEB5α + pXG10-SF-danAN M4) current work ML040
AS-161 (NEB5α + pXG10-SF-danAN M5) current work ML041
RN-7 (NEB5α + pXG10-SF-alaS) current work ML042
RN-16 (NEB5α + pXG10-SF-alaS M2) current work ML043
AS-75 (XL10-Gold + pNM46-PreS) current work ML044
RN-13 (XL10-Gold + pNM46-PreS-M1) current work ML045
RN-27 (XL10-Gold + pNM46-PreS-M2) current work ML046
AS-86 (DH5α + pGEM3-dnaN) current work ML047
AS - 46 (MG1655 + pEF21) current work ML048
AS - 47 (MG1655 + pEF21:Hfq) current work ML049
AS-132 (NEB5α + pXG10-SF-ubiD) current work ML050
AS-133 (NEB5α + pXG10-SF-dicA) current work ML051
AS-134 (NEB5α + pXG10-SF-rpsU-dnaG) current work ML052
AS-135 (NEB5α + pXG10-SF-ptsI) current work ML053
AS-136 (NEB5α + pXG10-SF-crr) current work ML054
AS-137 (NEB5α + pXG10-SF-ftsYE) current work ML055
RN-40 (MG1655 + tet-sacB cassate) Li et al., 2013 13 ML056
PAS-1 Phage lambda Susan Gottesman (NIH phage collection) N/A
PAS-2 Phage lambda cI- Kaiser, 1957 14 N/A
PAS-3 Phage lambda cI857:kan current work N/A
PAS-4 Phage lambda cIII tor864 Altuvia and Oppenheim, 1986 15 N/A
Phage lambda cI857 Sam7 stf::P1parS-kan current work N/A
Chemicals, peptides, and recombinant proteins
RIL-seq reagents Melamed et al., 2008 16 N/A
Tri-reagent Sigma Aldrich Cat#T9424-100ML
RNase A and RNase T1 Thermo Fisher Scientific Cat#EN0551
Acrylamdie 19:1 40% Bio-Lab Cat#000135233500
ULTRAhyb-Oligo Hybridization Buffer Thermo Fisher Cat#AM8663
γ-32P ATP Scientific Enco N/A
T4 Polynucleotide Kinase New England Biolabs Cat#M0201S
Microspin™ G-50 Columns Cytivia Cat#27533991
Mini-PROTEAN TGX Gels Bio-Rad Cat#4568086
Trans-blot turbo transfer pack Bio-Rad Cat#1704159
nitrocellulose membranes (Portran 0.2μm) Protran Cat#10401383
GlycoBlue Coprecipitant Thermo Fisher Cat#AM9516
Mph1103I Scientific Thermo Fisher Cat#ER0731
NheI Scientific New England Biolabs Cat#R3131S
HindIII New England Biolabs Cat#3104S
RiboRuler Low Range RNA ladder Thermo Fisher Cat#SM1831
Low Range ssRNA ladder Scientific New England Biolabs Cat#NO364S
Probe GT membrane Bio-Rad Cat#1620159
T7 RNA polymerase New England Biolabs Cat#M0251S
MMLV-RT Promega Cat#M1701
Mitomycin C Thermo Fisher Cat#BP25312
iTaq Universal Sybr Green Scientific Bio-Rad Cat#1725124
Recombanant RNase inhibitor Takara Cat#2313A
RNase T1 Boehringer N/A
DMS Fluka Cat#41610
RppH New England Biolabs Cat#M0356S
5′-Phosphate-Dependent Exonuclease (TeX) Lucigen Cat#TER51020
5-bromo-2′-deoxyuridine (BrdU) Sigma Aldrich Cat#19-160
SM-buffer Teknova Cat#S0249
Isopropyl-β-thiogalactoside (IPTG) Sigma Aldrich Cat#I6758
Critical commercial assays
QuikChange Lightning Site-Directed Mutagenesis Agilent Cat# 210519-S
ClearBand ECL western blot substrate Tivan Cat#CB-250
Clarity Max Western ECL Bio Rad Cat#1705062
Sequenase version 2.0 DNA Polymerase Thermo Fisher Cat#70775Y200UN
Bacterial DNA isolation kit Scientific Norgen Biotek Cat#17900
NEBuilder assembly master mix New England Biolabs Cat#MSS20AA
RNA Clean & Concentrator-5 Zymo research Cat#R1016
Turbo DNA-free kit Thermo Fisher Scientific Cat#AM2238
iScript cDNA Synthesis kit Bio-Rad Cat#1708891
Qubit dsDNA HS Assay kit Thermo Fisher Scientific Cat#Q32854
RNAprotect Bacteria Reagent Qiagen Cat#76506
Quick-RNA Fungal/Bacterial Microprep Kit Zymo Research Cat#R2010
RNA Library Prep kit Watchmaker Genomics Cat#7K0078-096
Deposited data
Unprocessed and uncompressed imaging data This Study DOI:10.17632/hbmnzwkk93.1
RIL-seq and RNA-seq Data This Study GEO: GSE279505
Synchronized RNA-seq Data This Study GEO: GSE298101
Experimental models: Organisms/strains
Oligonucleotides
RNA-seq oligos Table S5 N/A
sRNA Overexpression Constructs oligos Table S5 N/A
Cloning into pGEM-3 and GFP constructs oligos Table S5 N/A
qPCR oligos Table S5 N/A
Phage scarless mutation oligos Table S5 N/A
Northern probes oligos Table S5 N/A
Structural probing oligos Table S5 N/A
gBlocks Table S5 N/A
Recombinant DNA
pALA3047 (Plac-cfp-parB) Yao et al., 2021 7 N/A
pXG0 Urban et al., 2007 8 N/A
pXG10-SF Corcoran et al., 2012 9 N/A
pNM46 Walling et al., 2022 10 N/A
pCP20 Cherepanov et al., 1995 11 N/A
pGEM-3 Promega Corporation N/A
pKD46 Datsenko et al., 2000 12 N/A
pXG10-SF-danAN current work N/A
pXG10-SF-danAN M1 current work N/A
pXG10-SF-danAN M2 current work N/A
pXG10-SF-danAN M3 current work N/A
pXG10-SF-danAN M4 current work N/A
pXG10-SF-danAN M5 current work N/A
pXG10-SF-alaS current work N/A
pXG10-SF-alaS M2 current work N/A
pNM46-PreS current work N/A
pNM46-PreS-M1 current work N/A
pNM46-PreS-M2 current work N/A
pGEM3-dnaN current work N/A
pEF21 Faigenbaum-Romm et al., 2020 17 N/A
pEF21-Hfq Faigenbaum-Romm et al., 2020 17 N/A
pXG10-SF-ubiD current work N/A
pXG10-SF-dicA current work N/A
pXG10-SF-rpsU-dnaG current work N/A
pXG10-SF-ptsI current work N/A
pXG10-SF-crr current work N/A
pXG10-SF-ftsYE current work N/A
tet-sacB cassate Li et al., 2013 13 N/A
Software and algorithms
Python RILSeq package (version 0.82) Melamed et al., 2018 16 https://github.com/asafpr/RILseq
EcoCyc version 27.5 Karp et al., 2023 18 http://ecocyc.org
ImageJ software ImageJ http://rsb.info.nih.gov/ij
DESeq2 (version 1.36.0) Love et al., 2014 19 https://bioconductor.org/packages/devel/bioc/html/DESeq2.html
Rcircos library (version 1.2.2) Zhang et al., 2013 20 https://cloud.r-project.org/web/packages/RCircos/index.html
R (version 4.2.0) Team et al., 2016 21 https://www.R-project.org/
MEME tool (version 5.4.1) Bailey et al., 2009 22 https://meme-suite.org/meme/
MAST (version 5.4.1) Bailey et al., 1998 23 https://meme-suite.org/meme/doc/mast.html
Python (version 3.9) package matplotlib-venn (version 0.11.7) Hunter et al., 2007 24 https://pypi.org/project/matplotlib-venn/
Python (version 3.9) package matplotlib (version 3.5.1) Hunter et al., 2007 24 https://pypi.org/project/matplotlib/3.5.1/
Python (version 3.9) package seaborn (version 0.11.2) Waskom et al., 2021 25 https://seaborn.pydata.org/archive/0.11/index.html
Cytoscape (version 3.9.1) Shannon et al., 2003 26 https://github.com/cytoscape/cytoscape/releases/3.9.1/
MEGA11 (version 11.0.13) Tamura et al., 2021 27 https://www.megasoftware.net/
Kutools ExtendOffice https://www.extendoffice.com/product/kutools-for-excel.html
BLAST+ (version 2.12.0) Camacho et al., 2009 28 https://www.ncbi.nlm.nih.gov/books/NBK131777/
Easyfig (version 2.2.5) Sullivan et al., 2011 29 http://easyfig.sourceforge.net/
BWA (version 0.7.17) Li et al., 2009 30 https://github.com/lh3/bwa
SAMtools (version 1.9) Danecek et al., 2021 31 https://www.htslib.org/
BEDTools (version 2.28.0) Quinlan et al., 2010 32 https://bedtools.readth